Workflows

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69 Workflows visible to you, out of a total of 79
Work-in-progress

A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.

Type: Nextflow

Creator: Krisztian Papp

Submitter: Ross Thorne

Work-in-progress

A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.

Type: Nextflow

Creator: David F. Nieuwenhuijse, Alexey Sokolov

Submitter: Ross Thorne

Stable

Just the cleaning then assembly of all reads. TO explore further follow one of the paths described in "Global view" (WF 0)

Type: Galaxy

Creators: None

Submitter: johan Rollin

Stable

Mapping against all plant virus then make contig out of the mapped reads then blast them.

Type: Galaxy

Creators: None

Submitter: johan Rollin

Work-in-progress

Non-functional workflow to get a global view of possibilities for plant virus classification.

Type: Galaxy

Creators: None

Submitter: johan Rollin

Galaxy version of pre-processing of reads from COVID-19 samples. QC + human read cleaning Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh

Type: Galaxy

Creators: None

Submitter: ignacio eguinoa

Work-in-progress

Workflow to build different indices for different tools from a genome and transcriptome.

This workflow expects an (annotated) genome in GBOL ttl format.

Steps:

  • SAPP: rdf2gtf (genome fasta)
  • SAPP: rdf2fasta (transcripts fasta)
  • STAR index (Optional for Eukaryotic origin)
  • bowtie2 index
  • kallisto index

Type: Common Workflow Language

Creators: None

Submitter: Bart Nijsse

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