Available Pipelines

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20 sanger-tol/treeval

curation genome-alignment genome-assembly genomics quality-control synteny

Pipelines for the production of Treeval data

Version 1.1.1   Published 2 weeks ago

1 sanger-tol/ensemblgenedownload

download gene-annotation genomics indexing

Nextflow pipeline to download gene annotations from Ensembl onto the Tree of Life directory structure

Version 2.0.0   Published 1 month ago

1 sanger-tol/ensemblrepeatdownload

download formatting genomics

Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure

Version 2.0.0   Published 1 month ago

1 sanger-tol/insdcdownload

download genomics indexing

Nextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directories

Version 2.0.0   Published 1 month ago

3 sanger-tol/variantcalling

alignment genomics variant-calling

This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.

Version 1.1.3   Published 2 months ago

8 sanger-tol/readmapping

genomics read-alignment

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

Version 1.2.2   Published 2 months ago

19 sanger-tol/genomenote

genomics hic publications statistics

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

Version 1.2.0   Published 3 months ago

10 sanger-tol/blobtoolkit

blobtools decontamination genomehubs genomics

Nextflow pipeline for BlobToolKit for Sanger ToL production suite

Version 0.4.0   Published 3 months ago

2 sanger-tol/sequencecomposition

genomics kmer-frequency-count running-average shannon-entropy

Nextflow pipeline to extract statistics from a genome about its sequence composition

Version 1.0.0   Published 2 years ago

3 sanger-tol/ascc


A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.

No releases yet

3 sanger-tol/curationpretext

genomics hic

A Nextflow DSL2 pipeline for pretext generation in curation

No releases yet


gene-alignment genomics

An NF-core pipeline to alignment genesets against a given reference genome.

No releases yet

13 sanger-tol/genomeassembly

genome-assembly genomics

Implementation of ToL genome assembly workflows

No releases yet

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