Hi,
I'm a cetacean population geneticist in San Diego, CA, and I'm trying to use Illumina resequencing of nuclear loci (from capture-array enriched libraries) from 50-150 individuals to detect SNPs in the population, and determine the genotypes of the individuals. I use CLC Genomics Workbench to analyze the data, but have found that it (and other software that I've looked at) is focused only on finding SNPs in individual alignments to a reference sequence, not comparing across individual assemblies.
Does anyone have suggestions for how I can 1) assemble all of my reads from individuals to a set of reference sequences (CLC does this), 2) do SNP discovery based on variation in reads from the reference for each individual and each locus (CLC also does this), and then 3) compare the SNP positions across all individuals and loci to generate tables of SNP genotypes for each individual and position within each locus?
Thanks!
I'm a cetacean population geneticist in San Diego, CA, and I'm trying to use Illumina resequencing of nuclear loci (from capture-array enriched libraries) from 50-150 individuals to detect SNPs in the population, and determine the genotypes of the individuals. I use CLC Genomics Workbench to analyze the data, but have found that it (and other software that I've looked at) is focused only on finding SNPs in individual alignments to a reference sequence, not comparing across individual assemblies.
Does anyone have suggestions for how I can 1) assemble all of my reads from individuals to a set of reference sequences (CLC does this), 2) do SNP discovery based on variation in reads from the reference for each individual and each locus (CLC also does this), and then 3) compare the SNP positions across all individuals and loci to generate tables of SNP genotypes for each individual and position within each locus?
Thanks!
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