NGS RAD : Population Genomics on RAD data with a reference genome

Created: 2014-03-05 13:31:02 Last updated: 2014-06-10 09:11:35

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Analyse clean population SAM files (coming from alignment of FastQ from Stacks : Process Radtag tool for example) with a reference genome and population information

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Workflow Components

Inputs (2)

Name	Description
SAM file(s) (or archive) from Alignment on clean demultiplexed fastQ file
Population map

Steps (6)

Name	Tool	Description
Input dataset	None
Input dataset	None
STACKS : Reference map	dev-galaxy.genouest.org:9009/repos/cmonjeau/stacks_toolsuite/STACKSrefmap/1.0.0
STACKS : populations	dev-galaxy.genouest.org:9009/repos/cmonjeau/stacks_toolsuite/STACKSpopulation/1.0.0
Remove beginning	Remove beginning1
Transpose_tabular	transposeTabular

Outputs (27)

Name	Type
output	txt
catalogsnps	tabular
catalogalleles	tabular
catalogtags	tabular
total_output	zip
tags_output	zip
snps_output	zip
alleles_output	zip
matches_output	zip
output	txt
sumstatssum	tabular
sumstats	tabular
outfst	zip
outvcf	vcf
outphylip	phylip
outphyliplog	txt
outunphasedlog	txt
outfasta	fasta
outstructure	tabular
outplinkped	txt
outplinkmap	txt
outgenepop	txt
outphase	zip
outbeagle	zip
outmarkers	zip
out_file1	input
output	tabular

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Galaxy

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Ylebras

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Ylebras

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Information Statistics

893 viewings

625 downloads

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Citations (1)Version History

1. Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France, JOBIM 2013, 03 July 2013, https://www.e-biogenouest.org/resources/128

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