sars-cov-2-se-illumina-wgs-variant-calling/COVID-19-SE-WGS-ILLUMINA
View on GitHub
Download RO-Crate
Tests 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 |
|
| Single End Collection | Single End Collection | Illumina reads with fastqsanger encoding |
|
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 |
|
| fastp_html_report | fastp_html_report | n/a |
|
| mapped_reads | mapped_reads | n/a |
|
| markduplicates_stats | markduplicates_stats | n/a |
|
| markduplicates_reads | markduplicates_reads | n/a |
|
| preprocessing_and_mapping_reports | preprocessing_and_mapping_reports | n/a |
|
| realigned_deduplicated_mapped_reads | realigned_deduplicated_mapped_reads | n/a |
|
| realigned_deduplicated_mapped_reads_with_indel_quals | realigned_deduplicated_mapped_reads_with_indel_quals | n/a |
|
| called_variant | called_variant | n/a |
|
| soft_filtered_variants | soft_filtered_variants | n/a |
|
| annotated_variants | annotated_variants | n/a |
|
| annotated_variants_stats | annotated_variants_stats | n/a |
|
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
Creators and Submitter
Views: 1888 Downloads: 414
Created: 30th Aug 2021 at 17:00
Last updated: 30th Aug 2021 at 17:01
AttributionsNone
Related items
https://orcid.org/0000-0001-8271-5429
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: Not specified
