Stacks: an analysis tool set for population genomics
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Cites methods from "Stacks: an analysis tool set for po..."
...Availability: Software is written in Python and freely available at http://www.dereneaton.com/software/ Supplement: Scripts to completely reproduce all simulated and empirical analyses are available in the Supplementary Materials....
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Cites background or methods from "Stacks: an analysis tool set for po..."
...…mammals, making novel inferences regarding selection in natural populations in addition to measuring demographic parameters using neutral markers (Catchen et al. 2013b; Corander et al. 2013; De Wit & Palumbi 2013; Hess et al. 2013; Hyma & Fay 2013; Keller et al. 2013; Reitzel et al. 2013; Roda…...
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...The most comprehensive pipeline for handling GBS data is Stacks (Catchen et al. 2011), and in this issue, Catchen et al. (2013a) describe new features in Stacks to calculate population genomic statistics (such as FST and nucleotide diversity), create smoothed distributions using sliding window…...
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496 citations
References
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"Stacks: an analysis tool set for po..." refers methods in this paper
...Although reference genome aligners report reads aligned to both the positive and negative strand by the left-most genomic coordinate, pstacks will utilize the CIGAR string in the SAM file to reorient all reads such that their genomic alignment position is determined by the location of the restriction enzyme cut site....
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...Stacks can handle raw sequencing data in FASTA or FASTQ format to identify loci de novo and reads aligned against a reference genome in SAM (Li et al. 2009) format....
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...The pstacks program will read the CIGAR string (Li et al. 2009) from each alignment in the SAM file to determine whether the read contained an insertion, deletion or soft-masking [see Appendix S1, 1.2, Supporting information for information on CIGAR strings]....
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...Furthermore, SAMtools/BCFtools and GATK can call SNPs in multiple samples and can generate allele frequencies, but there is no built-in concept of populations....
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...Two of the most widely used are SAMtools/BCFtools (Li et al. 2009) and the Genome Analysis Toolkit (GATK, McKenna et al. 2010)....
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43,862 citations
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20,557 citations
"Stacks: an analysis tool set for po..." refers methods in this paper
...Two of the most widely used are SAMtools/BCFtools (Li et al. 2009) and the Genome Analysis Toolkit (GATK, McKenna et al. 2010)....
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20,335 citations
"Stacks: an analysis tool set for po..." refers methods in this paper
...Through the program pstacks, Stacks is able to use data from any alignment program that can produce SAM or BAM output files and has been extensively tested with Bowtie (Langmead et al. 2009), BWA (Li & Durbin 2009) and GSNAP (Wu & Nacu 2010)....
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