Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'
3.0

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Workflow Type: Galaxy

RAD-Seq Reference-based data analysis

Associated Tutorial

This workflows is part of the tutorial RAD-Seq Reference-based data analysis, available in the GTN

Thanks to...

Tutorial Author(s): Yvan Le Bras

Tutorial Contributor(s): Verena Moosmann, Helena Rasche, Saskia Hiltemann, Nicola Soranzo, Yvan Le Bras, Bérénice Batut, Björn Grüning, William Durand, Niall Beard, Wolfgang Maier

SEEK ID: https://workflowhub.eu/workflows/1665?version=1

Inputs

ID	Name	Description	Type
SRR034310.fastq.gz	EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz	n/a	File
Barcode_SRR034310.txt	https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt	n/a	File
Details_Barcode_Population_SRR034310.txt	https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt	n/a	File
Reference_genome_11_chromosomes.fasta	https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta	n/a	File

Steps

ID	Name	Description
10	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71
11	Map with BWA	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
12	Select	Grep1
13	Select	Grep1
14	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
15	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
16	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
17	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
18	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
19	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
20	Add column	addValue
21	Concatenate datasets	cat1
22	Cut	Cut1
23	Convert	Convert characters1
24	Regex Replace	toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0
25	Stacks: reference map	toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0
26	Stacks: populations	toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0
27	Summary Statistics	Summary_Statistics1
28	Sort	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
29	Count	Count1
30	Filter	Filter1
4	Stacks: process radtags	toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0
5	Stacks: process radtags	toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0
6	Stacks: process radtags	toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0
7	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
8	Select	Grep1
9	Select	Grep1