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81 lines
3.9 KiB
BibTeX
81 lines
3.9 KiB
BibTeX
@article{cock2010sanger,
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title={The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants},
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author={Cock, Peter JA and Fields, Christopher J and Goto, Naohisa and Heuer, Michael L and Rice, Peter M},
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journal={Nucleic acids research},
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volume={38},
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number={6},
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pages={1767--1771},
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year={2010},
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publisher={Oxford University Press}
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}
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@ARTICLE{Boyer2016-gq,
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title = "{obitools: a unix-inspired software package for DNA metabarcoding}",
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author = "Boyer, Fr{\'e}d{\'e}ric and Mercier, C{\'e}line and Bonin,
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Aur{\'e}lie and Le Bras, Yvan and Taberlet, Pierre and Coissac,
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Eric",
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abstract = "DNA metabarcoding offers new perspectives in biodiversity
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research. This recently developed approach to ecosystem study
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relies heavily on the use of next-generation sequencing (NGS)
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and thus calls upon the ability to deal with huge sequence data
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sets. The obitools package satisfies this requirement thanks to
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a set of programs specifically designed for analysing NGS data
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in a DNA metabarcoding context. Their capacity to filter and
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edit sequences while taking into account taxonomic annotation
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helps to set up tailor-made analysis pipelines for a broad range
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of DNA metabarcoding applications, including biodiversity
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surveys or diet analyses. The obitools package is distributed as
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an open source software available on the following website:
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http://metabarcoding.org/obitools. A Galaxy wrapper is available
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on the GenOuest core facility toolshed:
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http://toolshed.genouest.org.",
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journal = "Molecular ecology resources",
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publisher = "Wiley Online Library",
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volume = 16,
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number = 1,
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pages = "176--182",
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month = jan,
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year = 2016,
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url = "http://dx.doi.org/10.1111/1755-0998.12428",
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keywords = "PCR errors; biodiversity; next-generation sequencing; sequence
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analysis; taxonomic annotation",
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language = "en",
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issn = "1755-098X, 1755-0998",
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pmid = "25959493",
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doi = "10.1111/1755-0998.12428"
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}
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@article{Lipman1985-hw,
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abstract = {An algorithm was developed which facilitates the search for
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similarities between newly determined amino acid sequences and
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sequences already available in databases. Because of the
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algorithm's efficiency on many microcomputers, sensitive protein
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database searches may now become a routine procedure for
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molecular biologists. The method efficiently identifies regions
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of similar sequence and then scores the aligned identical and
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differing residues in those regions by means of an amino acid
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replacability matrix. This matrix increases sensitivity by giving
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high scores to those amino acid replacements which occur
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frequently in evolution. The algorithm has been implemented in a
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computer program designed to search protein databases very
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rapidly. For example, comparison of a 200-amino-acid sequence to
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the 500,000 residues in the National Biomedical Research
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Foundation library would take less than 2 minutes on a
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minicomputer, and less than 10 minutes on a microcomputer (IBM
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PC).},
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author = {Lipman, D J and Pearson, W R},
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date-added = {2023-01-26 15:17:10 +0100},
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date-modified = {2023-01-26 15:17:10 +0100},
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issn = {0036-8075},
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journal = {Science},
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month = mar,
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number = 4693,
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pages = {1435--1441},
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pmid = {2983426},
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title = {{Rapid and sensitive protein similarity searches}},
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url = {http://www.ncbi.nlm.nih.gov/pubmed/2983426},
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volume = 227,
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year = 1985,
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bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/2983426}}
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