NGS_tutorial

NGS data logistics

Associated Tutorial

This workflows is part of the tutorial NGS_tutorial, available in the GTN

Tutorial Author(s): Anton Nekrutenko, Marius van den Beek, Dave Clements, Daniel Blankenberg

Inputs

ID	Name	Description	Type
Accessions	#main/Accessions	n/a	File
Genome	#main/Genome	n/a	File

Steps

ID	Name	Description
2	Faster Download and Extract Reads in FASTQ	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0
3	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
4	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
5	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
6	MarkDuplicates	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
7	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
8	Realign reads	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
9	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
10	Insert indel qualities	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
11	Call variants	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
12	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
13	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
14	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

Outputs

ID	Name	Description	Type
_anonymous_output_1	#main/_anonymous_output_1	n/a	File
_anonymous_output_10	#main/_anonymous_output_10	n/a	File
_anonymous_output_11	#main/_anonymous_output_11	n/a	File
_anonymous_output_12	#main/_anonymous_output_12	n/a	File
_anonymous_output_13	#main/_anonymous_output_13	n/a	File
_anonymous_output_14	#main/_anonymous_output_14	n/a	File
_anonymous_output_15	#main/_anonymous_output_15	n/a	File
_anonymous_output_16	#main/_anonymous_output_16	n/a	File
_anonymous_output_17	#main/_anonymous_output_17	n/a	File
_anonymous_output_18	#main/_anonymous_output_18	n/a	File
_anonymous_output_19	#main/_anonymous_output_19	n/a	File
_anonymous_output_2	#main/_anonymous_output_2	n/a	File
_anonymous_output_20	#main/_anonymous_output_20	n/a	File
_anonymous_output_21	#main/_anonymous_output_21	n/a	File
_anonymous_output_22	#main/_anonymous_output_22	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File
_anonymous_output_5	#main/_anonymous_output_5	n/a	File
_anonymous_output_6	#main/_anonymous_output_6	n/a	File
_anonymous_output_7	#main/_anonymous_output_7	n/a	File
_anonymous_output_8	#main/_anonymous_output_8	n/a	File
_anonymous_output_9	#main/_anonymous_output_9	n/a	File

Version History

Added/updated 4 files

Open master 3c00116

Added/updated 4 files

Frozen 2.0 aacd515