NDLI: dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

Content Provider	PubMed Central
Author	Puritz, Jonathan B. Hollenbeck, Christopher M. Gold, John R.
Editor	Spivakov, Mikhail
Copyright Year	2014
Abstract	Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.
Related Links	http://dx.doi.org/10.7717/peerj.431
Starting Page	431
File Format	PDF
ISSN	21678359
e-ISSN	21678359
Journal	PeerJ
Volume Number	2
Language	English
Publisher	PeerJ Inc.
Publisher Date	2014-06-01
Access Restriction	Open
Rights Holder	PeerJ Inc.
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Neuroscience Medicine Biochemistry, Genetics and Molecular Biology Agricultural and Biological Sciences

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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