ERGA DataQC HiFi v2409 (WF0)
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Run on GalaxyThe workflow takes a HiFi reads collection, runs FastQC and SeqKit, filters with Cutadapt, and creates a MultiQC report. The main outputs are a collection of filtred reads, a report with raw and filtered reads stats, and a table with raw reads stats.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| HiFi raw reads collection | #main/HiFi raw reads collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | FastQC HiFi raw | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 |
| 2 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1 |
| 3 | SeqKit HiFi raw | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.8.1+galaxy0 |
| 4 | MultiQC HiFi | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0 |
| 5 | SeqKit HiFi | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| HiFi trimmed collection | #main/HiFi trimmed collection | n/a |
|
| SeqKit HiFi raw table | #main/SeqKit HiFi raw table | n/a |
|
Version History
Version 2 (latest) Created 18th Sep 2024 at 14:14 by Diego De Panis
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Version 1 (earliest) Created 6th Oct 2023 at 14:17 by Diego De Panis
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Version-1558378a
Creators and SubmitterViews: 3469 Downloads: 259 Runs: 38
Created: 6th Oct 2023 at 14:17
Last updated: 18th Sep 2024 at 14:15
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Related items
Teams: ERGA Assembly
Organizations: IZW
Welcome to the ERGA Space!
Here we collect, curate and develop pipelines to assemble and annotation reference-quality genomes for all eukaryotic life.
For Genome Assembly pipelines head to our Assembly Team
For Genome Annotation pipelines head to our Annotation Team
Development, discussions and issue tracking takes place in the ERGA github repo
If you would like to join ...
Teams: ERGA Assembly, ERGA Annotation
Web page: https://www.erga-biodiversity.eu/
A collection of workflows and pipelines developed as part of the ERGA consortium
Space: ERGA
Public web page: https://www.erga-biodiversity.eu/
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output a scaffolded primary assembliy and alternate contigs, with the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4
Maintainers: Tom Brown, Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, HiFi, Hi-C
