Workflows

What is a Workflow?
529 Workflows visible to you, out of a total of 572
Stable

HiC scaffolding pipeline

Snakemake pipeline for scaffolding of a genome using HiC reads using yahs.

Prerequisites

This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:

snakemake --use-conda --cores N

where N is number of cores to use. There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring the cluster.json file run:

./run_cluster ...

Type: Snakemake

Creator: Tom Brown

Submitter: Tom Brown

DOI: 10.48546/workflowhub.workflow.796.1

Purge dups

This snakemake pipeline is designed to be run using as input a contig-level genome and pacbio reads. This pipeline has been tested with snakemake v7.32.4. Raw long-read sequencing files and the input contig genome assembly must be given in the config.yaml file. To execute the workflow run:

snakemake --use-conda --cores N

Or configure the cluster.json and run using the ./run_cluster command

Type: Snakemake

Creator: Tom Brown

Submitter: Tom Brown

DOI: 10.48546/workflowhub.workflow.506.2

Stable

HiC contact map generation

Snakemake pipeline for the generation of .pretext and .mcool files for visualisation of HiC contact maps with the softwares PretextView and HiGlass, respectively.

Prerequisites

This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:

snakemake --use-conda

There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring ...

Type: Snakemake

Creator: Tom Brown

Submitter: Tom Brown

DOI: 10.48546/workflowhub.workflow.795.1

No description specified

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics. Updates November 2023. Inputs: reads as fastqsanger.gz (not fastq.gz), and assembly.fasta. New default settings for BUSCO: lineage = eukaryota; for Quast: lineage = eukaryotes, genome = large. Reports assembly stats into a table called metrics.tsv, including selected metrics from Fasta Stats, and read coverage; reports BUSCO versions and dependencies; and displays these tables in the workflow ...

Type: Galaxy

Creators: Gareth Price, Anna Syme

Submitter: Johan Gustafsson

Stable

gene2phylo

gene2phylo is a snakemake pipeline for batch phylogenetic analysis of a given set of input genes.

Contents

Setup

The pipeline is written in Snakemake and uses conda to install the necessary tools.

It is strongly recommended to install conda using Mambaforge. See details here ...

Type: Unrecognized workflow type

Creators: None

Submitter: Oliver White

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

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

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 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

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