Workflows

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736 Workflows visible to you, out of a total of 791
sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE

Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade

Type: Galaxy

Creators: Peter van Heusden, Peter van Heusden

Submitter: WorkflowHub Bot

sars-cov-2-variation-reporting/COVID-19-VARIATION-REPORTING

This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.

Type: Galaxy

Creators: Wolfgang Maier, Wolfgang Maier

Submitter: WorkflowHub Bot

sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.110.7

bacterial-genome-assembly/main

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

Type: Galaxy

Creators: Abromics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

quality-and-contamination-control/main

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

How Usable Are Published Permeability Data?
Stable

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

KNIME workflow to gather ChEMBL permeability data
Stable
No description specified

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

ERGA HiC Pri Scaffolding+QC YaHS v2409 (WF4)
Stable

The workflow takes trimmed HiC forward and reverse reads, and Pri/Alt assemblies to produce a scaffolded primary assembliy (and alternate contigs) using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

ERGA HiFi PriAlt Purge+QC v2409 (WF3)
Stable

The workflow takes a trimmed HiFi reads collection, Pri/Alt contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Pri and Alt contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1163.1

ERGA HiFi-only Assembly+QC Hifiasm v2409 (WF2)
Stable

The workflow takes a trimmed HiFi reads collection, and max coverage depth (calculated from WF1) to run Hifiasm in HiFi solo mode. It produces a Pri/Alt assembly, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1162.1

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