Stacks RAD-seq de novo workflow
Version 1

Workflow Type: Galaxy

workflow-denovo-stacks

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • population map in text format

Steps and outputs

ustacks:

  • input reads go to ustacks.
  • ustacks assembles the reads into matching stacks (hypothetical alleles).
  • The outputs are in a collection called something like: Stacks2: ustacks on data 21, data 20, and others Loci and polymorphism. Click on this to see the files:
  • for each sample, assembled loci (tsv format), named e.g. sample_CAAC.tags
  • for each sample, model calls from each locus (tsv format), named e.g. sample_CAAC.snps
  • for each sample, haplotypes/alleles recorded from each locus (tsv format), named e.g. sample_CAAC.alleles
  • Please see sections 6.1 to 6.4 in https://catchenlab.life.illinois.edu/stacks/manual/#ufiles for a full description.

cstacks:

  • cstacks will merge stacks into a catalog of consensus loci.
  • The outputs are in a collection called something like Stacks2: cstacks on data 3, data 71, and others Catalog of loci. Click on this to see the three files, each in tsv format: catalog.tags catalog.snps catalog.alleles

sstacks:

  • sstacks will compare each sample to the loci in the catalog.
  • The outputs are in a collection called something like Stacks2: sstacks on data 3, data 76, and others Matches to the catalog.Click on this to see the files: There is one file for each sample, named e.g. sample_CAAC.matches, in tsv format.

tsv2bam:

  • Conversion to BAM format
  • Reads from each sample are now aligned to each locus, and the tsv2bam tool will convert this into a bam file for each sample.
  • The outputs are in a collection called something like Stacks2: tsv2bam on data 3, data 94, and others Matches to the catalog.Click on this to see the files: There is one file for each sample, named e.g sample_CAAC.matches, in BAM format.

gstacks:

  • Catalog of loci in fasta format
  • Variant calls in VCF format

populations:

  • Locus consensus sequences in fasta format
  • Snp calls, in VCF format
  • Haplotypes, in VCF format
  • Summary statistics

denovo

Inputs

ID Name Description Type
Population map Population map n/a n/a
popmap popmap runtime parameter for tool Stacks2: sstacks n/a
input_type input_type runtime parameter for tool Stacks2: tsv2bam n/a
kernel_smoothing kernel_smoothing runtime parameter for tool Stacks2: populations n/a
options_filtering options_filtering runtime parameter for tool Stacks2: populations n/a
options_filtering options_filtering runtime parameter for tool Stacks2: populations n/a
options_usage options_usage runtime parameter for tool Stacks2: populations n/a
popmap popmap runtime parameter for tool Stacks2: populations n/a

Steps

ID Name Description
0 Input dataset collection
1 Population map
2 Stacks2: ustacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_ustacks/stacks2_ustacks/2.55+galaxy3
3 Stacks2: cstacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks/stacks2_cstacks/2.55+galaxy2
4 Stacks2: sstacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_sstacks/stacks2_sstacks/2.55+galaxy2
5 Stacks2: tsv2bam toolshed.g2.bx.psu.edu/repos/iuc/stacks2_tsv2bam/stacks2_tsv2bam/2.55+galaxy2
6 Stacks2: gstacks toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy2
7 Stacks2: populations toolshed.g2.bx.psu.edu/repos/iuc/stacks2_populations/stacks2_populations/2.55+galaxy2

Outputs

ID Name Description Type
tabs tabs n/a
output_log output_log n/a
catalog catalog n/a
output_log output_log n/a
matches matches n/a
output_log output_log n/a
bams bams n/a
output_log output_log n/a
gstacks_out gstacks_out n/a
output_log output_log n/a
output_log output_log n/a
out_haplotypes out_haplotypes n/a
out_hapstats out_hapstats n/a
out_populations_log_distribs out_populations_log_distribs n/a
out_sumstats_sum out_sumstats_sum n/a
out_sumstats out_sumstats n/a
out_phistats out_phistats n/a
out_phistats_sum out_phistats_sum n/a
out_fststats_sum out_fststats_sum n/a
out_fasta_strict out_fasta_strict n/a
out_vcf_haplotypes_snps out_vcf_haplotypes_snps n/a
out_vcf_haplotypes_haps out_vcf_haplotypes_haps n/a
out_structure out_structure n/a

Version History

v1.0 (earliest) Created 31st May 2022 at 08:39 by Anna Syme

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