Workflows

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731 Workflows visible to you, out of a total of 781
ERGA DataQC Illumina v2309 (WF0)
Stable

The workflow takes a paired-reads collection (like illumina WGS or HiC), runs FastQC and SeqKit, trims with Fastp, and creates a MultiQC report. The main outputs are a paired collection of trimmed reads, a report with raw and trimmed reads stats, and a table with raw reads stats.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.601.1

skim2rrna
Stable

skim2rrna

skim2rrna is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal genes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

Type: Snakemake

Creators: None

Submitter: Oliver White

skim2mt
Stable

skim2mt

skim2mt is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

Type: Snakemake

Creators: None

Submitter: Oliver White

dada2/main

dada2 amplicon analysis for paired end data

The workflow has three main outputs:

  • the sequence table (output of makeSequenceTable)
  • the taxonomy (output of assignTaxonomy)
  • the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)

Type: Galaxy

Creators: Matthias Bernt, UFZ Leipzig

Submitter: WorkflowHub Bot

ERGA ONT+Illumina Assembly+QC NextDenovo+HyPo v2403 (WF2)
Work-in-progress

The workflow takes raw ONT reads and trimmed Illumina WGS paired reads collections, the ONT raw stats table (calculated from WF1) and the estimated genome size (calculated from WF1) to run NextDenovo and subsequently polish the assembly with HyPo. It produces collapsed assemblies (unpolished and polished) and runs all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

ERGA ONT+Illumina Assembly+QC Flye+HyPo v2403 (WF2)
Stable

The workflow takes raw ONT reads and trimmed Illumina WGS paired reads collections, and the estimated genome size and Max depth (both calculated from WF1) to run Flye and subsequently polish the assembly with HyPo. It produces collapsed assemblies (unpolished and polished) and runs all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

score-assemblies
Stable

score-assemblies

A Snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina sequencing.

The workflow includes the following programs:

...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.786.1

ont-assembly-snake
Stable

ont-assembly-snake

A Snakemake wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data, using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

Included programs

read filtering assembly long read polishing short read polishing reference-based polishing
Filtlong
...

Type: Snakemake

Creator: Peter Menzel

Submitter: Peter Menzel

DOI: 10.48546/workflowhub.workflow.787.1

Wound Healing Scrath Assay Image Analysis
Work-in-progress

This project is about the automated quantification of wound healing in high-throughput microscopy scratch assays.

Type: Galaxy

Creator: Christian Tischer

Submitter: Yi Sun

Lysozyme in water full version, using REMOTE dataset, two workers, data_persistence False

Lysozyme in water full COMPSs application run at MareNostrum IV, using full dataset with two workers

Type: COMPSs

Creator: Rosa M Badia

Submitter: RaĆ¼l Sirvent

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