4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information

BMC Bioinformatics
Francisco Pina-MartinsOctávio S Paulo

Abstract

Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task. Here we describe 4Pipe4, a 454 data analysis pipeline particularly focused on SNP detection when no reference or strain information is available. It uses a command line interface to automatically call other programs, parse their outputs and summarize the results. The variation detection routine is built-in in the program itself. Despite being optimized for SNP mining in 454 EST data, it is flexible enough to automate the analysis of genomic data or even data from other NGS technologies. 4Pipe4 will output several HTML formatted reports with metrics on man...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Jan 1, 2008·Nature Methods·Stephan C Schuster
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 26, 2009·BMC Bioinformatics·Alexie PapanicolaouDavid G Heckel
Mar 17, 2010·BMC Bioinformatics·Aakrosh RatanWebb Miller
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
May 2, 2013·Nucleic Acids Research·Harm NijveenBen Vosman
Nov 19, 2014·Nucleic Acids Research·Raluca UricaruPierre Peterlongo

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Citations

Dec 15, 2017·Nature·Richard Van Noorden
Dec 1, 2017·Nature·Richard Van Noorden
Oct 6, 2018·Genome Biology·Alexandre SouvorovDavid J Lipman

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Methods Mentioned

BETA
genotyping

Software Mentioned

mira
DIAL
4Pipe4rc
kisSnp
SAMtools
SNP2
Blast2GO
AtlasSNP2
Sequence Cleaner
linux

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