Workflows

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80 Workflows visible to you, out of a total of 83

Stable

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container

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Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

Stable

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container

...

Type: Nextflow

Creator: José Mª Fernández

Submitter: Laura Rodriguez-Navas

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

Stable

Metagenomic dataset taxonomic classification using kraken2

Type: Galaxy

Creators: None

Submitter: johan Rollin

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