sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA

Workflow Type: Galaxy
Tests: Passing

COVID-19: variation analysis on WGS SE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.

Inputs

ID Name Description Type
NC_045512.2 FASTA sequence of SARS-CoV-2 NC_045512.2 FASTA sequence of SARS-CoV-2 Fasta sequence for Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
  • File
Single End Collection Single End Collection Illumina reads with fastqsanger encoding
  • File[]

Steps

ID Name Description
2 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
3 Bowtie2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2
4 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
5 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
6 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
7 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
8 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
9 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
10 SnpEff eff covid19 version toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19

Outputs

ID Name Description Type
preprocessed_reads preprocessed_reads n/a
  • File
fastp_html_report fastp_html_report n/a
  • File
mapped_reads mapped_reads n/a
  • File
markduplicates_stats markduplicates_stats n/a
  • File
markduplicates_reads markduplicates_reads n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
realigned_deduplicated_mapped_reads realigned_deduplicated_mapped_reads n/a
  • File
realigned_deduplicated_mapped_reads_with_indel_quals realigned_deduplicated_mapped_reads_with_indel_quals n/a
  • File
called_variant called_variant n/a
  • File
soft_filtered_variants soft_filtered_variants n/a
  • File
annotated_variants annotated_variants n/a
  • File
annotated_variants_stats annotated_variants_stats n/a
  • File

Version History

Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo

No revision comments

Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

No revision comments

help Creators and Submitter
Creators
Not specified
Additional credit

Wolfgang Maier

Submitter
License
Activity

Views: 799   Downloads: 9

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

help Attributions

None

Brought to you by:

Powered by
(v.1.13.3)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH