obitools4/doc/book.bib

@article{cock2010sanger,
  title={The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants},
  author={Cock, Peter JA and Fields, Christopher J and Goto, Naohisa and Heuer, Michael L and Rice, Peter M},
  journal={Nucleic acids research},
  volume={38},
  number={6},
  pages={1767--1771},
  year={2010},
  publisher={Oxford University Press}
}

@ARTICLE{Boyer2016-gq,
  title     = "{obitools: a unix-inspired software package for DNA metabarcoding}",
  author    = "Boyer, Fr{\'e}d{\'e}ric and Mercier, C{\'e}line and Bonin,
               Aur{\'e}lie and Le Bras, Yvan and Taberlet, Pierre and Coissac,
               Eric",
  abstract  = "DNA metabarcoding offers new perspectives in biodiversity
               research. This recently developed approach to ecosystem study
               relies heavily on the use of next-generation sequencing (NGS)
               and thus calls upon the ability to deal with huge sequence data
               sets. The obitools package satisfies this requirement thanks to
               a set of programs specifically designed for analysing NGS data
               in a DNA metabarcoding context. Their capacity to filter and
               edit sequences while taking into account taxonomic annotation
               helps to set up tailor-made analysis pipelines for a broad range
               of DNA metabarcoding applications, including biodiversity
               surveys or diet analyses. The obitools package is distributed as
               an open source software available on the following website:
               http://metabarcoding.org/obitools. A Galaxy wrapper is available
               on the GenOuest core facility toolshed:
               http://toolshed.genouest.org.",
  journal   = "Molecular ecology resources",
  publisher = "Wiley Online Library",
  volume    =  16,
  number    =  1,
  pages     = "176--182",
  month     =  jan,
  year      =  2016,
  url       = "http://dx.doi.org/10.1111/1755-0998.12428",
  keywords  = "PCR errors; biodiversity; next-generation sequencing; sequence
               analysis; taxonomic annotation",
  language  = "en",
  issn      = "1755-098X, 1755-0998",
  pmid      = "25959493",
  doi       = "10.1111/1755-0998.12428"
}


@article{Lipman1985-hw,
	abstract = {An algorithm was developed which facilitates the search for
              similarities between newly determined amino acid sequences and
              sequences already available in databases. Because of the
              algorithm's efficiency on many microcomputers, sensitive protein
              database searches may now become a routine procedure for
              molecular biologists. The method efficiently identifies regions
              of similar sequence and then scores the aligned identical and
              differing residues in those regions by means of an amino acid
              replacability matrix. This matrix increases sensitivity by giving
              high scores to those amino acid replacements which occur
              frequently in evolution. The algorithm has been implemented in a
              computer program designed to search protein databases very
              rapidly. For example, comparison of a 200-amino-acid sequence to
              the 500,000 residues in the National Biomedical Research
              Foundation library would take less than 2 minutes on a
              minicomputer, and less than 10 minutes on a microcomputer (IBM
              PC).},
	author = {Lipman, D J and Pearson, W R},
	date-added = {2023-01-26 15:17:10 +0100},
	date-modified = {2023-01-26 15:17:10 +0100},
	issn = {0036-8075},
	journal = {Science},
	month = mar,
	number = 4693,
	pages = {1435--1441},
	pmid = {2983426},
	title = {{Rapid and sensitive protein similarity searches}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/2983426},
	volume = 227,
	year = 1985,
	bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/2983426}}


@ARTICLE{Shehzad2012-pn,
  title     = "{Carnivore diet analysis based on next-generation sequencing:
               Application to the leopard cat (Prionailurus bengalensis) in
               Pakistan}",
  author    = "Shehzad, Wasim and Riaz, Tiayyba and Nawaz, Muhammad A and
               Miquel, Christian and Poillot, Carole and Shah, Safdar A and
               Pompanon, Francois and Coissac, Eric and Taberlet, Pierre",
  journal   = "Molecular ecology",
  publisher = "Wiley Online Library",
  volume    =  21,
  number    =  8,
  pages     = "1951--1965",
  year      =  2012,
  url       = "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x",
  issn      = "0962-1083"
}


@ARTICLE{Riaz2011-gn,
  title    = "{ecoPrimers: inference of new DNA barcode markers from whole
              genome sequence analysis}",
  author   = "Riaz, Tiayyba and Shehzad, Wasim and Viari, Alain and Pompanon,
              Fran{\c c}ois and Taberlet, Pierre and Coissac, Eric",
  abstract = "Using non-conventional markers, DNA metabarcoding allows
              biodiversity assessment from complex substrates. In this article,
              we present ecoPrimers, a software for identifying new barcode
              markers and their associated PCR primers. ecoPrimers scans whole
              genomes to find such markers without a priori knowledge.
              ecoPrimers optimizes two quality indices measuring taxonomical
              range and discrimination to select the most efficient markers
              from a set of reference sequences, according to specific
              experimental constraints such as marker length or specifically
              targeted taxa. The key step of the algorithm is the
              identification of conserved regions among reference sequences for
              anchoring primers. We propose an efficient algorithm based on
              data mining, that allows the analysis of huge sets of sequences.
              We evaluate the efficiency of ecoPrimers by running it on three
              different sequence sets: mitochondrial, chloroplast and bacterial
              genomes. Identified barcode markers correspond either to barcode
              regions already in use for plants or animals, or to new potential
              barcodes. Results from empirical experiments carried out on a
              promising new barcode for analyzing vertebrate diversity fully
              agree with expectations based on bioinformatics analysis. These
              tests demonstrate the efficiency of ecoPrimers for inferring new
              barcodes fitting with diverse experimental contexts. ecoPrimers
              is available as an open source project at:
              http://www.grenoble.prabi.fr/trac/ecoPrimers.",
  journal  = "Nucleic acids research",
  volume   =  39,
  number   =  21,
  pages    = "e145",
  month    =  nov,
  year     =  2011,
  url      = "http://dx.doi.org/10.1093/nar/gkr732",
  language = "en",
  issn     = "0305-1048, 1362-4962",
  pmid     = "21930509",
  doi      = "10.1093/nar/gkr732",
  pmc      = "PMC3241669"
}


@ARTICLE{Seguritan2001-tg,
  title    = "{FastGroup: a program to dereplicate libraries of 16S rDNA
              sequences}",
  author   = "Seguritan, V and Rohwer, F",
  abstract = "BACKGROUND: Ribosomal 16S DNA sequences are an essential tool for
              identifying and classifying microbes. High-throughput DNA
              sequencing now makes it economically possible to produce very
              large datasets of 16S rDNA sequences in short time periods,
              necessitating new computer tools for analyses. Here we describe
              FastGroup, a Java program designed to dereplicate libraries of
              16S rDNA sequences. By dereplication we mean to: 1) compare all
              the sequences in a data set to each other, 2) group similar
              sequences together, and 3) output a representative sequence from
              each group. In this way, duplicate sequences are removed from a
              library. RESULTS: FastGroup was tested using a library of
              single-pass, bacterial 16S rDNA sequences cloned from
              coral-associated bacteria. We found that the optimal strategy for
              dereplicating these sequences was to: 1) trim ambiguous bases
              from the 5' end of the sequences and all sequence 3' of the
              conserved Bact517 site, 2) match the sequences from the 3' end,
              and 3) group sequences > or =97\% identical to each other.
              CONCLUSIONS: The FastGroup program simplifies the dereplication
              of 16S rDNA sequence libraries and prepares the raw sequences for
              subsequent analyses.",
  journal  = "BMC bioinformatics",
  volume   =  2,
  pages    = "9",
  month    =  oct,
  year     =  2001,
  url      = "http://dx.doi.org/10.1186/1471-2105-2-9",
  language = "en",
  issn     = "1471-2105",
  pmid     = "11707150",
  doi      = "10.1186/1471-2105-2-9",
  pmc      = "PMC59723"
}