Workflows

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2 Workflows matching the given criteria: (Clear all filters)

Tool:

(Hybrid) Metagenomics workflow

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Work-in-progress

Workflow (hybrid) metagenomic assembly and binning

Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
FastQC (control)
fastp (quality trimming)
kraken2 (taxonomy)
bbmap contamination filter
Workflow Longread Quality:
NanoPlot (control)
filtlong (quality trimming)
kraken2 (taxonomy)
minimap2 contamination filter
Kraken2 taxonomic classification of FASTQ reads
SPAdes/Flye (Assembly)
Pilon/Medaka/PyPolCA (Assembly polishing)
QUAST (Assembly ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke

Submitter: Bart Nijsse

Created: 14th Jun 2022 at 09:14, Last updated: 18th Dec 2024 at 10:14

Workflow 3: AMR - SeqSero2/SISTR

Seq4AMR

Work-in-progress

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada. Doi: 10.3389/fmicb.2020.00549

tool	version	license
SeqSero2	1.2.1	GNU GPL v2.0
...

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Created: 24th Nov 2022 at 13:42, Last updated: 9th Sep 2024 at 09:23

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