Available Pipelines
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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 4 weeks ago
1 sanger-tol/ensemblrepeatdownload
Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure
Version 2.0.0 Published 4 weeks ago
1 sanger-tol/insdcdownload
Nextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directories
Version 2.0.0 Published 4 weeks 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 1 month ago
8 sanger-tol/readmapping
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 1 month 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 2 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
20 sanger-tol/treeval
curation genome-alignment genome-assembly genomics quality-control synteny
Pipelines for the production of Treeval data
Version 1.1.0 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
A Nextflow DSL2 pipeline for pretext generation in curation
No releases yet
1 sanger-tol/longreadmag
No releases yet
sanger-tol/treevalhiglassdigest
Workflow to ingest TreeVal output into HiGlass Kubernetes for Sanger Tree of Life.
No releases yet
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