dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
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 wi...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2014-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/431.pdf |
| _version_ | 1797425571898064896 |
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| author | Jonathan B. Puritz Christopher M. Hollenbeck John R. Gold |
| author_facet | Jonathan B. Puritz Christopher M. Hollenbeck John R. Gold |
| author_sort | Jonathan B. Puritz |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:18:02Z |
| format | Article |
| id | doaj.art-d1b9dd524235425c8e21f3c6ec27e0c1 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:18:02Z |
| publishDate | 2014-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-d1b9dd524235425c8e21f3c6ec27e0c12023-12-02T22:00:14ZengPeerJ Inc.PeerJ2167-83592014-06-012e43110.7717/peerj.431431dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organismsJonathan B. Puritz0Christopher M. Hollenbeck1John R. Gold2Marine Genomics Laboratory, Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, TX, USAMarine Genomics Laboratory, Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, TX, USAMarine Genomics Laboratory, Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, TX, USARestriction-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.https://peerj.com/articles/431.pdfRADseqPopulation genomicsBioinformaticsMolecular ecologyNext-generation sequencing |
| spellingShingle | Jonathan B. Puritz Christopher M. Hollenbeck John R. Gold dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms PeerJ RADseq Population genomics Bioinformatics Molecular ecology Next-generation sequencing |
| title | dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms |
| title_full | dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms |
| title_fullStr | dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms |
| title_full_unstemmed | dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms |
| title_short | dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms |
| title_sort | ddocent a radseq variant calling pipeline designed for population genomics of non model organisms |
| topic | RADseq Population genomics Bioinformatics Molecular ecology Next-generation sequencing |
| url | https://peerj.com/articles/431.pdf |
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