obitools4/doc/build/_book/search.json

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    "text": "Preface\nThe first version of OBITools started to be developed in 2005. This was at the beginning of the DNA metabarcoding story at the Laboratoire d’Ecologie Alpine (LECA) in Grenoble. At that time, with Pierre Taberlet and François Pompanon, we were thinking about the potential of this new methodology under development. PIerre and François developed more the laboratory methods, while I was thinking more about the tools for analysing the sequences produced. Two ideas were behind this development. I wanted something modular, and something easy to extend. To achieve the first goal, I decided to implement obitools as a suite of unix commands mimicking the classic unix commands but dedicated to sequence files. The basic unix commands are very useful for automatically manipulating, parsing and editing text files. They work in flow, line by line on the input text. The result is a new text file that can be used as input for the next command. Such a design makes it possible to quickly develop a text processing pipeline by chaining simple elementary operations. The OBITools are the exact counterpart of these basic Unix commands, but the basic information they process is a sequence (potentially spanning several lines of text), not a single line of text. Most OBITools consume sequence files and produce sequence files. Thus, the principles of chaining and modularity are respected. In order to be able to easily extend the OBITools to keep up with our evolving ideas about processing DNA metabarcoding data, it was decided to develop them using an interpreted language: Python. Python 2, the version available at the time, allowed us to develop the OBITools efficiently. When parts of the algorithms were computationally demanding, they were implemented in C and linked to the Python code. Even though Python is not the most efficient language available, even though computers were not as powerful as they are today, the size of the data we could produce using 454 sequencers or early solexa machines was small enough to be processed in a reasonable time.\nThe first public version of obitools was OBITools2 (Boyer et al. 2016), this was actually a cleaned up and documented version of OBITools that had been running at LECA for years and was not really distributed except to a few collaborators. This is where OBITools started its public life from then on. The DNA metabarcoding spring schools provided and still provide user training every year. But OBITools2 soon suffered from two limitations: it was developed in Python2, which was increasingly abandoned in favour of Python3, and the data size kept increasing with the new illumina machines. Python’s intrinsic slowness coupled with the increasing size of the datasets made OBITools computation times increasingly long. The abandonment of all maintenance of Python2 by its developers also imposed the need for a new version of OBITools.\nOBITools3 was the first response to this crisis. Developed and maintained by Céline Mercier, OBITools3 attempted to address several limitations of OBITools2. It is a complete new code, mainly developed in Python3, with most of the lower layer code written in C for efficiency. OBITools3 has also abandoned text files for binary files for the same reason of efficiency. They have been replaced by a database structure that keeps track of every operation performed on the data.\nHere we present OBITools4 which can be seen as a return to the origins of OBITools. While OBITools3 offered traceability of analyses, which is in line with the concept of open science, and faster execution, OBITools2 was more versatile and not only usable for the analysis of DNA metabarcoding data. OBITools4 is the third full implementation of OBITools. The idea behind this new version is to go back to the original design of OBITools which ran on text files containing sequences, like the classic Unix commands, but running at least as fast as OBITools3 and taking advantage of the multicore architecture of all modern laptops. For this, the idea of relying on an interpreted language was 
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    "title": "The OBITools",
    "section": "Aims of OBITools",
    "text": "Aims of OBITools\nDNA metabarcoding is an efficient approach for biodiversity studies (Taberlet et al. 2012). Originally mainly developed by microbiologists (e.g. Sogin et al. 2006), it is now widely used for plants (e.g. Sønstebø et al. 2010; Yoccoz et al. 2012; Parducci et al. 2012) and animals from meiofauna (e.g. Chariton et al. 2010; Baldwin et al. 2013) to larger organisms (e.g. Andersen et al. 2012; Thomsen et al. 2012). Interestingly, this method is not limited to sensu stricto biodiversity surveys, but it can also be implemented in other ecological contexts such as for herbivore (e.g. Valentini et al. 2009; Kowalczyk et al. 2011) or carnivore (e.g. Deagle, Kirkwood, and Jarman 2009; Shehzad et al. 2012) diet analyses.\nWhatever the biological question under consideration, the DNA metabarcoding methodology relies heavily on next-generation sequencing (NGS), and generates considerable numbers of DNA sequence reads (typically million of reads). Manipulation of such large datasets requires dedicated programs usually running on a Unix system. Unix is an operating system, whose first version was created during the sixties. Since its early stages, it is dedicated to scientific computing and includes a large set of simple tools to efficiently process text files. Most of those programs can be viewed as filters extracting information from a text file to create a new text file. These programs process text files as streams, line per line, therefore allowing computation on a huge dataset without requiring a large memory. Unix programs usually print their results to their standard output (stdout), which by default is the terminal, so the results can be examined on screen. The main philosophy of the Unix environment is to allow easy redirection of the stdout either to a file, for saving the results, or to the standard input (stdin) of a second program thus allowing to easily create complex processing from simple base commands. Access to Unix computers is increasingly easier for scientists nowadays. Indeed, the Linux operating system, an open source version of Unix, can be freely installed on every PC machine and the MacOS operating system, running on Apple computers, is also a Unix system. The OBITools programs imitate Unix standard programs because they usually act as filters, reading their data from text files or the stdin and writing their results to the stdout. The main difference with classical Unix programs is that text files are not analyzed line per line but sequence record per sequence record (see below for a detailed description of a sequence record). Compared to packages for similar purposes like mothur (Schloss et al. 2009) or QIIME (Caporaso et al. 2010), the OBITools mainly rely on filtering and sorting algorithms. This allows users to set up versatile data analysis pipelines (Figure 1), adjustable to the broad range of DNA metabarcoding applications. The innovation of the OBITools is their ability to take into account the taxonomic annotations, ultimately allowing sorting and filtering of sequence records based on the taxonomy.\n\n\n\n\nAndersen, Kenneth, Karen Lise Bird, Morten Rasmussen, James Haile, Henrik Breuning-Madsen, Kurt H Kjaer, Ludovic Orlando, M Thomas P Gilbert, and Eske Willerslev. 2012. “Meta-barcoding of ëdirtı́DNA from soil reflects vertebrate biodiversity.” Molecular Ecology 21 (8): 1966–79.\n\n\nBaldwin, Darren S, Matthew J Colloff, Gavin N Rees, Anthony A Chariton, Garth O Watson, Leon N Court, Diana M Hartley, et al. 2013. “Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils.” Molecular Ecology 22 (6): 1746–58. https://doi.org/10.1111/mec.12190.\n\n\nCaporaso, J Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, et al. 2010. “QIIME allows analysis of high-throughput community sequencing data.” Nature Methods 7 (5): 335–36. https://doi.org/10.1038/nmeth.f.303.\n\n\nChariton, Anthony A, Anthony C Roach, Stuart L Simpson, and Graeme E Batley. 2010. “Influ
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    "section": "1.1 Availability of the OBITools",
    "text": "1.1 Availability of the OBITools\nThe OBITools are open source and protected by the CeCILL 2.1 license.\nAll the sources of the OBITools4 can be downloaded from the metabarcoding git server (https://git.metabarcoding.org)."
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    "text": "1.2 Prerequisites\nThe OBITools4 are developped using the GO programming language, we stick to the latest version of the language, today the 1.21.41.21.4. If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. Some parts of the soft are also written in C, therefore a recent C compiler is also requested, GCC on Linux or Windows, the Developer Tools on Mac.\nWhatever the installation you decide for, you will have to ensure that a C compiler is available on your system."
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    "section": "1.3 Installation with the install script",
    "text": "1.3 Installation with the install script\nAn installation script that compiles the new OBITools on your Unix-like system is available online. The easiest way to run it is to copy and paste the following command into your terminal\n\ncurl -L https://metabarcoding.org/obitools4/install.sh | bash\n\nBy default, the script installs the OBITools commands and other associated files into the /usr/local directory. The names of the commands in the new OBITools4 are mostly identical to those in OBITools2. Therefore, installing the new OBITools may hide or delete the old ones. If you want both versions to be available on your system, the installation script offers two options:\n\n-i, –install-dir Directory where OBITools are installed (as example use /usr/local not /usr/local/bin).\n-p, –obitools-prefix Prefix added to the OBITools command names if you want to have several versions of obitools at the same time on your system (as example -p g will produce gobigrep command instead of obigrep).\n\nYou can use these options by following the installation command:\n\ncurl -L https://metabarcoding.org/obitools4/install.sh | \\\n      bash -s -- --install-dir test_install --obitools-prefix k\n\nIn this case, the binaries will be installed in the test_install directory and all command names will be prefixed with the letter k. Thus obigrep will be named kobigrep."
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    "text": "1.4 Compilation from sources"
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    "section": "2.1 The DNA sequence data",
    "text": "2.1 The DNA sequence data\nSequences can be stored following various format. OBITools knows some of them. The central formats for sequence files manipulated by OBITools scripts are the FASTA and FASTQ format. OBITools extends the both these formats by specifying a syntax to include in the definition line data qualifying the sequence. All file formats use the IUPAC code for encoding nucleotides.\nMoreover these two formats that can be used as input and output formats, OBITools4 can read the following format :\n\nEBML flat file format (use by ENA)\nGenbank flat file format\necoPCR output files\n\n\n2.1.1 The IUPAC Code\nThe International Union of Pure and Applied Chemistry (IUPAC) defined the standard code for representing protein or DNA sequences.\n\n\n\nCode\nNucleotide\n\n\n\n\nA\nAdenine\n\n\nC\nCytosine\n\n\nG\nGuanine\n\n\nT\nThymine\n\n\nU\nUracil\n\n\nR\nPurine (A or G)\n\n\nY\nPyrimidine (C, T, or U)\n\n\nM\nC or A\n\n\nK\nT, U, or G\n\n\nW\nT, U, or A\n\n\nS\nC or G\n\n\nB\nC, T, U, or G (not A)\n\n\nD\nA, T, U, or G (not C)\n\n\nH\nA, T, U, or C (not G)\n\n\nV\nA, C, or G (not T, not U)\n\n\nN\nAny base (A, C, G, T, or U)\n\n\n\n\n\n2.1.2 The FASTA sequence format\nThe FASTA format is certainly the most widely used sequence file format. This is certainly due to its great simplicity. It was originally created for the Lipman and Pearson FASTA program. OBITools use in more of the classical FASTA format an extended version of this format where structured data are included in the title line.\nIn FASTA format a sequence is represented by a title line beginning with a > character and the sequences by itself following the IUPAC code. The sequence is usually split other severals lines of the same length (expect for the last one)\n>my_sequence this is my pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\nThis is no special format for the title line excepting that this line should be unique. Usually the first word following the > character is considered as the sequence identifier. The end of the title line corresponding to a description of the sequence. Several sequences can be concatenated in a same file. The description of the next sequence is just pasted at the end of the record of the previous one\n>sequence_A this is my first pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n>sequence_B this is my second pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n>sequence_C this is my third pretty sequence\nACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT\nGTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT\nAACGACGTTGCAGTACGTTGCAGT\n\n2.1.2.1 File extensions\nThere is no standard file extension for a FASTA file, but .fa and .fasta, are commonly used.\n\n\n\n2.1.3 The FASTQ sequence format1\nThe FASTQ format is a text file format for storing both biological sequences (only nucleic acid sequences) and the associated sequence quality scores. Every nucleotide of the sequence and its associated quality score are each encoded by a single ASCII character. This format was originally developed by the Wellcome Trust Sanger Institute to link a FASTA sequence file to the corresponding quality data, but is now became the de facto standard for storing results from high-throughput sequencers (Cock et al. 2010).\nOBITools considers that a FASTQ file uses four lines to encode a sequence record.\n\nLine 1 begins with a ‘@’ character and is followed by a sequence identifier and an optional description (like a FASTA title line).\nLine 2 is the sequence letters, in upper or lower case, but OBITools only write sequences as lower cases.\nLine 3 begins with a ‘+’ character and is optionally followed by the same sequence identifier (and any description) again.\nLin
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    "section": "2.2 The taxonomy files",
    "text": "2.2 The taxonomy files\nMany OBITools are able to take into account taxonomic data. This is done by specifying a directory containing all :doc:NCBI taxonomy dump files <./taxdump>."
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    "section": "2.3 The sample description file",
    "text": "2.3 The sample description file\nA key file for OBITools4 is the file describing all samples (PCR) analyzed in the processed sequencing library file. This file, often called the ngsfilter file, is a tab separated values (TSV) file. The format of this file is exactly identical to that used in OBITools2 and OBITools4.\n{tsv, .smaller} wolf_diet    13a_F730603      aattaac  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F wolf_diet    15a_F730814      gaagtag  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F wolf_diet    26a_F040644      gaatatc  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F wolf_diet    29a_F260619      gcctcct  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F\nAt least six columns must be present in every line of the file.\n\nThe first column contains the name of the experience:\nAn experiment name groups a set of sample together. Sequences belonging to the experiment are tagged with an attribute experiment containing the name of the experiment in their annotation.\nThe second column contains the sample identifier in the experiment\nThe sample identifier must be unique in the experiment. The obimultiplex and obitagpcr commands add to all the sequences bellonging to the same sample an attribute sample containing the sample identifier\nThe third column contains description of the tag used to identify sequences corresponding to this sample\nThe fourth column contains the forward primer sequence\nThe fifth column contains the reverse primer sequence\nThe sixth column must always contain the character F (full length)\n\n\n\n\n\nCock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and Peter M Rice. 2010. “The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa/Illumina FASTQ Variants.” Nucleic Acids Research 38 (6): 1767–71."
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    "section": "3.1 Wolves’ diet based on DNA metabarcoding",
    "text": "3.1 Wolves’ diet based on DNA metabarcoding\nThe data used in this tutorial correspond to the analysis of four wolf scats, using the protocol published in Shehzad et al. (2012) for assessing carnivore diet. After extracting DNA from the faeces, the DNA amplifications were carried out using the primers TTAGATACCCCACTATGC and TAGAACAGGCTCCTCTAG amplifiying the 12S-V5 region (Riaz et al. 2011), together with a wolf blocking oligonucleotide.\nThe complete data set can be downloaded here: the tutorial dataset\nOnce the data file is downloaded, using a UNIX terminal unarchive the data from the tgz file.\n\ntar zxvf wolf_diet.tgz\n\nThat command create a new directory named wolf_data containing every required data files:\n\nfastq <fastq> files resulting of aGA IIx (Illumina) paired-end (2 x 108 bp) sequencing assay of DNA extracted and amplified from four wolf faeces:\n\nwolf_F.fastq\nwolf_R.fastq\n\nthe file describing the primers and tags used for all samples sequenced:\n\nwolf_diet_ngsfilter.txt The tags correspond to short and specific sequences added on the 5' end of each primer to distinguish the different samples\n\nthe file containing the reference database in a fasta format:\n\ndb_v05_r117.fasta This reference database has been extracted from the release 117 of EMBL using obipcr\n\n\n\n\n\nTo not mix raw data and processed data a new directory called results is created.\n\nmkdir results"
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    "section": "3.2 Step by step analysis",
    "text": "3.2 Step by step analysis\n\n3.2.1 Recover full sequence reads from forward and reverse partial reads\nWhen using the result of a paired-end sequencing assay with supposedly overlapping forward and reverse reads, the first step is to recover the assembled sequence.\nThe forward and reverse reads of the same fragment are at the same line position in the two fastq files obtained after sequencing. Based on these two files, the assembly of the forward and reverse reads is done with the obipairing utility that aligns the two reads and returns the reconstructed sequence.\nIn our case, the command is:\n\nobipairing --min-identity=0.8 \\\n           --min-overlap=10 \\\n           -F wolf_data/wolf_F.fastq \\\n           -R wolf_data/wolf_R.fastq \\\n           > results/wolf.fastq \n\nThe --min-identity and --min-overlap options allow discarding sequences with low alignment quality. If after the aligment, the overlaping parts of the reads is shorter than 10 base pairs or the similarity over this aligned region is below 80% of identity, in the output file, the forward and reverse reads are not aligned but concatenated, and the value of the mode attribute in the sequence header is set to joined instead of alignment.\n\n\n3.2.2 Remove unaligned sequence records\nUnaligned sequences (:pymode=joined) cannot be used. The following command allows removing them from the dataset:\n\nobigrep -p 'annotations.mode != \"join\"' \\\n        results/wolf.fastq > results/wolf.ali.fastq\n\nThe -p requires a go like expression. annotations.mode != \"join\" means that if the value of the mode annotation of a sequence is different from join, the corresponding sequence record will be kept.\nThe first sequence record of wolf.ali.fastq can be obtained using the following command line:\n\nhead -n 4 results/wolf.ali.fastq\n\nThe folling piece of code appears on thew window of tour terminal.\n@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {\"ali_dir\":\"left\",\"ali_length\":62,\"mode\":\"alignment\",\"pairing_mismatches\":{\"(T:26)->(G:13)\":62,\"(T:34)->(G:18)\":48},\"score\":484,\"score_norm\":0.968,\"seq_a_single\":46,\"seq_ab_match\":60,\"seq_b_single\":46}\nccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg\n+\nCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\\RYU\\\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC\n\n\n3.2.3 Assign each sequence record to the corresponding sample/marker combination\nEach sequence record is assigned to its corresponding sample and marker using the data provided in a text file (here wolf_diet_ngsfilter.txt). This text file contains one line per sample, with the name of the experiment (several experiments can be included in the same file), the name of the tags (for example: aattaac if the same tag has been used on each extremity of the PCR products, or aattaac:gaagtag if the tags were different), the sequence of the forward primer, the sequence of the reverse primer, the letter T or F for sample identification using the forward primer and tag only or using both primers and both tags, respectively (see obimultiplex for details).\n\nobimultiplex -t wolf_data/wolf_diet_ngsfilter.txt \\\n             -u results/unidentified.fastq \\\n             results/wolf.ali.fastq \\\n             > results/wolf.ali.assigned.fastq\n\nThis command creates two files:\n\nunidentified.fastq containing all the sequence records that were not assigned to a sample/marker combination\nwolf.ali.assigned.fastq containing all the sequence records that were properly assigned to a sample/marker combination\n\nNote that each sequence record of the wolf.ali.assigned.fastq file contains only the barcode sequence as the sequences of primers and tags are removed by the obimultiplex program. Information concerning the experiment, sample, primers and tags is added as attributes in the sequence header.\nFor instance, the first sequence record of wolf.ali.assigned.fastq is:\n@HELIUM_000
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    "title": "4  Specifying the data input to OBITools commands",
    "section": "4.1 Specifying input format",
    "text": "4.1 Specifying input format\nFive sequence formats are accepted for input files. Fasta (Section 2.1.2) and Fastq (Section 2.1.3) are the main ones, EMBL and Genbank allow the use of flat files produced by these two international databases. The last one, ecoPCR, is maintained for compatibility with previous OBITools and allows to read ecoPCR outputs as sequence files.\n\n--ecopcr : Read data following the ecoPCR output format.\n--embl Read data following the EMBL flatfile format.\n--genbank Read data following the Genbank flatfile format.\n\nSeveral encoding schemes have been proposed for quality scores in Fastq format. Currently, OBITools considers Sanger encoding as the standard. For reasons of compatibility with older datasets produced with Solexa sequencers, it is possible, by using the following option, to force the use of the corresponding quality encoding scheme when reading these older files.\n\n--solexa Decodes quality string according to the Solexa specification. (default: false)"
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    "section": "5.1 Specifying output format",
    "text": "5.1 Specifying output format\nOnly two output sequence formats are supported by OBITools, Fasta and Fastq. Fastq is used when output sequences are associated with quality information. Otherwise, Fasta is the default format. However, it is possible to force the output format by using one of the following two options. Forcing the use of Fasta results in the loss of quality information. Conversely, when the Fastq format is forced with sequences that have no quality data, dummy qualities set to 40 for each nucleotide are added.\n\n--fasta-output Read data following the ecoPCR output format.\n--fastq-output Read data following the EMBL flatfile format.\n\nOBITools allows multiple input files to be specified for a single command.\n\n--no-order When several input files are provided, indicates that there is no order among them. (default: false). Using such option can increase a lot the processing of the data."
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    "section": "5.2 The Fasta and Fastq annotations format",
    "text": "5.2 The Fasta and Fastq annotations format\nOBITools extend the Fasta and Fastq formats by introducing a format for the title lines of these formats allowing to annotate every sequence. While the previous version of OBITools used an ad-hoc format for these annotation, this new version introduce the usage of the standard JSON format to store them.\nOn input, OBITools automatically recognize the format of the annotations, but two options allows to force the parsing following one of them. You should normally not need to use these options.\n\n--input-OBI-header FASTA/FASTQ title line annotations follow OBI format. (default: false)\n--input-json-header FASTA/FASTQ title line annotations follow json format. (default: false)\n\nOn output, by default annotation are formatted using the new JSON format. For compatibility with previous version of OBITools and with external scripts and software, it is possible to force the usage of the previous OBITools format.\n\n--output-OBI-header|-O output FASTA/FASTQ title line annotations follow OBI format. (default: false)\n--output-json-header output FASTA/FASTQ title line annotations follow json format. (default: false)"
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    "section": "6.1 Helpful options",
    "text": "6.1 Helpful options\n\n--help, -h\n\nDisplay a friendly help message.\n\n\n--no-progressbar"
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    "text": "6.2 System related options\nManaging parallel execution of tasks\nA new feature of OBITools V4 is the ability to run multiple tasks in parallel, reading files, calculating on the data, formatting and writing the results. Each of these tasks can itself be parallelized by dividing the data into batches and running the calculation on several batches in parallel. This allows the overall calculation time of an OBITools command to be reduced considerably. The parameters organizing the parallel calculation are determined automatically to use the maximum capacity of your computer. But in some circumstances, it is necessary to override these default settings either to try to optimize the computation on a given machine, or to limit the OBITools to using only a part of the computational capacity. There are two options for doing this.\n\n--max-cpu\n\nOBITools V4 are able to run in parallel on all the CPU cores available on the computer. It is sometime required to limit the computation to a smaller number of cores. That option specify the maximum number of cores that the OBITools command can use. This behaviour can also be set up using the OBIMAXCPU environment variable.\n\n\n--workers, -w\nIf your computer has 8 cores, but you want to limit OBITools to use only two of them you have several solution:\n\nIf you want to set the limit for a single execution you can use the –max-cpu option\nobiconvert --max-cpu 2 --fasta-output data.fastq > data.fasta\nor you can precede the command by setting the environment variable OBIMAXCPU\nOBIMAXCPU=2 obiconvert --fasta-output data.fastq > data.fasta\nIf you want to set the limit to your complete session, you have to export OBIMAXCPU\nexport OBIMAXCPU=2 \nall the following OBITools commands will be limited to use at max 2 CPU cores.\nIf all the time you want to impose this limit, you must include the above export command in your .bashrc file.\n\nOBITools debuging related options\n--debug"
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    "section": "7.1 Variables usable in the expression",
    "text": "7.1 Variables usable in the expression\n\nsequence is the sequence object on which the expression is evaluated.\nannotationsis a map object containing every annotations associated to the currently processed sequence."
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    "section": "7.2 Function defined in the language",
    "text": "7.2 Function defined in the language\n\nInstrospection functions\n\nlen(x)\n\nIt is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like annotations, the number of elements in an array. The reurned value is an int.\n\ncontains(map,key)\n\nTests if the map contains a value assciated to key\n\n\n\n\nCast functions\n\nint(x)\n\nConverts if possible the x value to an integer value. The function returns an int.\n\nnumeric(x)\n\nConverts if possible the x value to a float value. The function returns a float.\n\nbool(x)\n\nConverts if possible the x value to a boolean value. The function returns a bool.\n\n\n\n\nString related functions\n\nprintf(format,...)\n\nAllows to combine several values to build a string. format follows the classical C printf syntax. The function returns a string.\n\nsubspc(x)\n\nsubstitutes every space in the x string by the underscore (_) character. The function returns a string.\n\n\n\n\nCondition function\n\nifelse(condition,val1,val2)\n\nThe condition value has to be a bool value. If it is true the function returns val1, otherwise, it is returning val2.\n\n\n\n\n7.2.1 Sequence analysis related function\n\ncomposition(sequence)\n\nThe nucleotide composition of the sequence is returned as as map indexed by a, c, g, or t and each value is the number of occurrences of that nucleotide. A fifth key others accounts for all others symboles.\n\ngcskew(sequence)\n\nComputes the excess of g compare to c of the sequence, known as the GC skew.\nSkewGC=G−CG+C\nSkew_{GC}=\\frac{G-C}{G+C}"
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    "text": "7.3 Accessing to the sequence annotations\nThe annotations variable is a map object containing all the annotations associated to the currently processed sequence. Index of the map are the attribute names. It exists to possibillities to retreive an annotation. It is possible to use the classical [] indexing operator, putting the attribute name quoted by double quotes between them.\nannotations[\"direction\"]\nThe above code retreives the direction annotation. A second notation using the dot (.) is often more convenient.\nannotations.direction\nSpecial attributes of the sequence are accessible only by dedicated methods of the sequence object.\n\nThe sequence identifier : Id()\nTHe sequence definition : Definition()\n\nsequence.Id()"
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    "text": "8.1 obipcr\n\nReplace the ecoPCR original OBITools"
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    "text": "11.1 obipairing\n\nReplace the illuminapairedends original OBITools\n\n\nAlignment procedure\nobipairing is introducing a new alignment algorithm compared to the illuminapairedend command of the OBITools V2. Nethertheless this new algorithm has been design to produce the same results than the previous, except in very few cases.\nThe new algorithm is a two-step procedure. First, a FASTN-type algorithm (Lipman and Pearson 1985) identifies the best offset between the two matched readings. This identifies the region of overlap.\nIn the second step, the matching regions of the two reads are extracted along with a flanking sequence of Δ\\Delta base pairs. The two subsequences are then aligned using a “one side free end-gap” dynamic programming algorithm. This latter step is only called if at least one mismatch is detected by the FASTP step.\nUnless the similarity between the two reads at their overlap region is very low, the addition of the flanking regions in the second step of the alignment ensures the same alignment as if the dynamic programming alignment was performed on the full reads.\n\n\nThe scoring system\nIn the dynamic programming step, the match and mismatch scores take into account the quality scores of the two aligned nucleotides. By taking these into account, the probability of a true match can be calculated for each aligned base pair.\nIf we consider a nucleotide read with a quality score QQ, the probability of misreading this base (PEP_E) is : PE=10−Q10\nP_E = 10^{-\\frac{Q}{10}}\n\nThus, when a given nucleotide XX is observed with the quality score QQ. The probability that XX is really an XX is :\nP(X=X)=1−PE\nP(X=X) = 1 - P_E\n\nOtherwise, XX is actually one of the three other possible nucleotides (XE1X_{E1}, XE2X_{E2} or XE3X_{E3}). If we suppose that the three reading error have the same probability :\nP(X=XE1)=P(X=XE3)=P(X=XE3)=PE3\nP(X=X_{E1}) = P(X=X_{E3}) = P(X=X_{E3}) = \\frac{P_E}{3}\n\nAt each position in an alignment where the two nucleotides X1X_1 and X2X_2 face each other (not a gapped position), the probability of a true match varies depending on whether X1=X2X_1=X_2, an observed match, or X1≠X2X_1 \\neq X_2, an observed mismatch.\nProbability of a true match when X1=X2X_1=X_2\nThat probability can be divided in two parts. First X1X_1 and X2X_2 have been correctly read. The corresponding probability is :\nPTM=(1−PE1)(1−PE2)=(1−10−Q110)(1−10−Q210)\n\\begin{aligned}\nP_{TM} &= (1- PE_1)(1-PE_2)\\\\ \n       &=(1 - 10^{-\\frac{Q_1}{10} } )(1 - 10^{-\\frac{Q_2}{10}} )\n\\end{aligned}\n\nSecondly, a match can occure if the true nucleotides read as X1X_1 and X2X_2 are not X1X_1 and X2X_2 but identical.\nP(X1==XE1)∩P(X2==XE1)=PE1PE29P(X1==XEx)∩P(X2==XEx)=PE1PE23\n\\begin{aligned}\nP(X_1==X_{E1}) \\cap P(X_2==X_{E1}) &= \\frac{P_{E1} P_{E2}}{9} \\\\\nP(X_1==X_{Ex}) \\cap P(X_2==X_{Ex}) & = \\frac{P_{E1} P_{E2}}{3}\n\\end{aligned}\n\nThe probability of a true match between X1X_1 and X2X_2 when X1=X2X_1 = X_2 an observed match :\nP(MATCH|X1=X2)=(1−PE1)(1−PE2)+PE1PE23\n\\begin{aligned}\nP(MATCH | X_1 = X_2) = (1- PE_1)(1-PE_2) + \\frac{P_{E1} P_{E2}}{3}\n\\end{aligned}\n\nProbability of a true match when X1≠X2X_1 \\neq X_2\nThat probability can be divided in three parts.\n\nX1X_1 has been correctly read and X2X_2 is a sequencing error and is actually equal to X1X_1. Pa=(1−PE1)PE23\nP_a =  (1-P_{E1})\\frac{P_{E2}}{3}\n\nX2X_2 has been correctly read and X1X_1 is a sequencing error and is actually equal to X2X_2. Pb=(1−PE2)PE13\nP_b =  (1-P_{E2})\\frac{P_{E1}}{3}\n\nX1X_1 and X2X_2 corresponds to sequencing error but are actually the same base XExX_{Ex} Pc=2PE1PE29\nP_c = 2\\frac{P_{E1} P_{E2}}{9}\n\n\nConsequently : P(MATCH|X1≠X2)=(1−PE1)PE23+(1−PE2)PE13+2PE1PE29\n\\begin{aligned}\nP(MATCH | X_1 \\neq X_2) =  (1-P_{E1})\\frac{P_{E2}}{3} +  (1-P_{E2})\\frac{P_{E1}}{3} + 2\\frac{P_{E1} P_{E2}}{9}\n\\end{aligned}\n\nProbability of a match under the random model\nThe second considered model is a pure random model where every base is equiprobable, hence ha
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    "text": "11.5 obiuniq\n\n\n\n\nLipman, D J, and W R Pearson. 1985. “Rapid and sensitive protein similarity searches.” Science 227 (4693): 1435–41. http://www.ncbi.nlm.nih.gov/pubmed/2983426."
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    "section": "12.1 obigrep – filters sequence files according to numerous conditions",
    "text": "12.1 obigrep – filters sequence files according to numerous conditions\nThe obigrep command is somewhat analogous to the standard Unix grep command. It selects a subset of sequence records from a sequence file. A sequence record is a complex object consisting of an identifier, a set of attributes (a key, defined by its name, associated with a value), a definition, and the sequence itself. Instead of working text line by text line like the standard Unix tool, obigrep selection is done sequence record by sequence record. A large number of options allow you to refine the selection on any element of the sequence. obigrep allows you to specify multiple conditions simultaneously (which take on the value TRUE or FALSE) and only those sequence records which meet all conditions (all conditions are TRUE) are selected. obigrep is able to work on two paired read files. The selection criteria apply to one or the other of the readings in each pair depending on the mode chosen (--paired-mode option). In all cases the selection is applied in the same way to both files, thus maintaining their consistency.\n\n12.1.1 The options usable with obigrep\n\n12.1.1.1 Selecting sequences based on their caracteristics\nSequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.\nSelection based on the sequence\nSequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (e.g AACCTT). But the usage of regular patterns allows for looking for more complex pattern. As example, A[TG]C+G matches a A, followed by a T or a G, then one or several C and endly a G.\n\n--sequence|-s PATTERN\n\nRegular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available here.\n\nExamples:\n\nSelects only the sequence records that contain an EcoRI restriction site.\n\n\nobigrep -s 'GAATTC' seq1.fasta > seq2.fasta\n: Selects only the sequence records that contain a stretch of at least 10 A.\nobigrep -s 'A{10,}' seq1.fasta > seq2.fasta\n: Selects only the sequence records that do not contain ambiguous nucleotides.\nobigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta\n\n--min-count | -c COUNT\n\nonly sequences reprensenting at least COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to 11.\n\n--max-count | -C COUNT\n\nonly sequences reprensenting no more than COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to 11.\n\nExamples\n\nSelecting sequence records representing at least five reads in the dataset.\n\n\nobigrep -c 5 data_SPER01.fasta > data_norare_SPER01.fasta"
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    "text": "13.1 obicount\nobicount counts the number of sequence records, the sum of the count attributes, and the sum of the length of all the sequences.\nExample:\nobicount seq.fasta  \nPrints the number of sequence records contained in the seq.fasta file and the sum of their count attributes.\nOptions specific to the command\n\n--reads|-r Prints read counts.\n--symbols|-s Prints symbol counts.\n--variants|-v Prints variant counts."
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    "text": "13.3 obifind\n\nReplace the ecofind original OBITools."
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    "text": "BioSequence\nThe BioSequence class is used to represent biological sequences. It allows for storing : - the sequence itself as a []byte - the sequencing quality score as a []byte if needed - an identifier as a string - a definition as a string - a set of (key, value) pairs in a map[sting]interface{}\nBioSequence is defined in the obiseq module and is included using the code\nimport (\n    \"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq\"\n)\n\nCreating new instances\nTo create new instance, use\n\nMakeBioSequence(id string, sequence []byte, definition string) obiseq.BioSequence\nNewBioSequence(id string, sequence []byte, definition string) *obiseq.BioSequence\n\nBoth create a BioSequence instance, but when the first one returns the instance, the second returns a pointer on the new instance. Two other functions MakeEmptyBioSequence, and NewEmptyBioSequence do the same job but provide an uninitialized objects.\n\nid parameters corresponds to the unique identifier of the sequence. It mist be a string constituted of a single word (not containing any space).\nsequence is the DNA sequence itself, provided as a byte array ([]byte).\ndefinition is a string, potentially empty, but usualy containing a sentence explaining what is that sequence.\n\nimport (\n    \"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq\"\n)\n\nfunc main() {\n    myseq := obiseq.NewBiosequence(\n        \"seq_GH0001\",\n        bytes.FromString(\"ACGTGTCAGTCG\"),\n        \"A short test sequence\",\n        )\n}\nWhen formated as fasta the parameters correspond to the following schema\n>id definition containing potentially several words\nsequence\n\n\nEnd of life of a BioSequence instance\nWhen an instance of BioSequence is no longer in use, it is normally taken over by the GO garbage collector. If you know that an instance will never be used again, you can, if you wish, call the Recycle method on it to store the allocated memory elements in a pool to limit the allocation effort when many sequences are being handled. Once the recycle method has been called on an instance, you must ensure that no other method is called on it.\n\n\nAccessing to the elements of a sequence\nThe different elements of an obiseq.BioSequence must be accessed using a set of methods. For the three main elements provided during the creation of a new instance methodes are :\n\nId() string\nSequence() []byte\nDefinition() string\n\nIt exists pending method to change the value of these elements\n\nSetId(id string)\nSetSequence(sequence []byte)\nSetDefinition(definition string)\n\nimport (\n    \"fmt\"\n    \"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq\"\n)\n\nfunc main() {\n    myseq := obiseq.NewBiosequence(\n        \"seq_GH0001\",\n        bytes.FromString(\"ACGTGTCAGTCG\"),\n        \"A short test sequence\",\n        )\n\n    fmt.Println(myseq.Id())\n    myseq.SetId(\"SPE01_0001\")\n    fmt.Println(myseq.Id())\n}\n\nDifferent ways for accessing an editing the sequence\nIf Sequence()and SetSequence(sequence []byte) methods are the basic ones, several other methods exist.\n\nString() string return the sequence directly converted to a string instance.\nThe Write method family allows for extending an existing sequence following the buffer protocol.\n\nWrite(data []byte) (int, error) allows for appending a byte array on 3’ end of the sequence.\nWriteString(data string) (int, error) allows for appending a string.\nWriteByte(data byte) error allows for appending a single byte.\n\n\nThe Clear method empties the sequence buffer.\nimport (\n    \"fmt\"\n    \"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq\"\n)\n\nfunc main() {\n    myseq := obiseq.NewEmptyBiosequence()\n\n    myseq.WriteString(\"accc\")\n    myseq.WriteByte(byte('c'))\n    fmt.Println(myseq.String())\n}\n\n\nSequence quality scores\nSequence quality scores cannot be initialized at the time of instance creation. You must use dedicated methods to add quality scores to a sequence.\nTo be coherent the length of both the DNA sequence and que quality score sequence must be equal. Bu
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    "text": "The sequence iterator\nThe pakage obiter provides an iterator mecanism for manipulating sequences. The main class provided by this package is obiiter.IBioSequence. An IBioSequence iterator provides batch of sequences.\n\nBasic usage of a sequence iterator\nMany functions, among them functions reading sequences from a text file, return a IBioSequence iterator. The iterator class provides two main methods:\n\nNext() bool\nGet() obiiter.BioSequenceBatch\n\nThe Next method moves the iterator to the next value, while the Get method returns the currently pointed value. Using them, it is possible to loop over the data as in the following code chunk.\nimport (\n    \"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats\"\n)\n\nfunc main() {\n    mydata := obiformats.ReadFastSeqFromFile(\"myfile.fasta\")\n       \n    for mydata.Next() {\n        data := mydata.Get()\n        //\n        // Whatever you want to do with the data chunk\n        //\n    }\n}\nAn obiseq.BioSequenceBatch instance is a set of sequences stored in an obiseq.BioSequenceSlice and a sequence number. The number of sequences in a batch is not defined. A batch can even contain zero sequences, if for example all sequences initially included in the batch have been filtered out at some stage of their processing.\n\n\nThe Pipable functions\nA function consuming a obiiter.IBioSequence and returning a obiiter.IBioSequence is of class obiiter.Pipable.\n\n\nThe Teeable functions\nA function consuming a obiiter.IBioSequence and returning two obiiter.IBioSequence instance is of class obiiter.Teeable."
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    "section": "A.1 Sequence attributes",
    "text": "A.1 Sequence attributes\nali_dir (string)\n\nSet by the obipairing tool\nThe attribute can contain 2 string values left or right.\n\nThe alignment generated by obipairing is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction ali_dir is set to left. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, ali_dir is set to right.\nali_length (int)\n\nSet by the obipairing tool\n\nLength of the aligned parts when merging forward and reverse reads\ncount (int)\n\nSet by the obiuniq tool\nGetter : method Count()\nSetter : method SetCount(int)\n\nThe count attribute indicates how-many strictly identical reads have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.\nThe Count() method allows to access to the count attribute as an integer value. If the count attribute is not defined for the given sequence, the value 1 is returned\nmerged_* (map[string]int)\n\nSet by the obiuniq tool\n\nThe -m option of the obiuniq tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when obiuniq is run after running obimultiplex. The actual name of the attribute depends on the name of the monitored attribute. If -m option is used with the attribute sample, then this attribute names merged_sample.\nmode (string)\n\nSet by the obipairing tool\nThe attribute can contain 2 string values join or alignment.\n\nobitag_ref_index (map[string]string)\n\nSet by the obirefidx tool.\n\nIt resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.\n   {\"0\":\"9606@Homo sapiens@species\",\n    \"2\":\"207598@Homininae@subfamily\",\n    \"3\":\"9604@Hominidae@family\",\n    \"8\":\"314295@Hominoidea@superfamily\",\n    \"10\":\"9526@Catarrhini@parvorder\",\n    \"12\":\"1437010@Boreoeutheria@clade\",\n    \"16\":\"9347@Eutheria@clade\",\n    \"17\":\"40674@Mammalia@class\",\n    \"22\":\"117571@Euteleostomi@clade\",\n    \"25\":\"7776@Gnathostomata@clade\",\n    \"29\":\"33213@Bilateria@clade\",\n    \"30\":\"6072@Eumetazoa@clade\"}\npairing_mismatches (map[string]string)\n\nSet by the obipairing tool\n\nseq_a_single (int)\n\nSet by the obipairing tool\n\nseq_ab_match (int)\n\nSet by the obipairing tool\n\nseq_b_single (int)\n\nSet by the obipairing tool\n\nscore (int)\n\nSet by the obipairing tool\n\nscore_norm (float)\n\nSet by the obipairing tool\nThe value ranges between 0 and 1.\n\nScore of the alignment between forward and reverse reads expressed as a fraction of identity."
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    "title": "References",
    "section": "",
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  }
]