ERGA DataQC HiFi v2505 (WF0)
View on GitHub
Download RO-Crate
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 | SeqKit HiFi raw | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.10.0+galaxy0 |
| 3 | Cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0 |
| 4 | SeqKit HiFi | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 5 | MultiQC HiFi | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
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 |
|
| html_report | #main/html_report | n/a |
|
Version History
Version 2 (latest) Created 18th Sep 2024 at 14:14 by Diego De Panis
Open
master62f2b97
Version 1 (earliest) Created 6th Oct 2023 at 14:17 by Diego De Panis
Initial commit
Frozen
Version-1558378a
Creators and Submitter
Views: 7203 Downloads: 943 Runs: 71
Created: 6th Oct 2023 at 14:17
Last updated: 1st Jun 2025 at 13:03
AttributionsNone
ERGA Assembly Galax...
ERGA Assembly Galax...
Biodiversity & ecol...
Related items
https://orcid.org/0000-0002-3679-9585
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/
This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and ...
Maintainers: Matúš Kalaš, Keiler Collier
Number of items: 28
Tags: Biodiversity, Ecology, Genome assembly, dna barcoding, natural history collections
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi or ONT reads and Illumina 3-dimensional Chromatin Confirmation Capture (Hi-C) reads
Executing the workflows collection will output a scaffolded primary assembly and alternate contigs, with the complete QC analyses
Please run the workflows in order: WF0', WF1, WF2, WF3, WF4
'Notice there is one for HiFi, one for ONT, and one for Illumina (WGS or Hi-C). Run according to your data. ...
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
