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treevalPipelines for the production of Treeval data
blobtoolkitNextflow pipeline for BlobToolKit for Sanger ToL production suite
readmappingNextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
gdaGenome Decomposition Analysis pipeline
genomeassemblyImplementation of ToL genome assembly workflows
tolqcToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.
variantcallingThis Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite.
tol-trackTracking scripts for Sanger Tree of Life sequencing data
asg-assembly-course-2021Notes for the 2021 Aquatic Symbiosis Genomics assembly course
sequencecompositionNextflow pipeline to extract statistics from a genome about its sequence composition
nf-core-pipelineGuidelines and subworkflows for Nextflow pipeline development in Sanger ToL
tol-qcScripts to generate ToLQC reports for the Sanger Tree of Life programme
vectorDBadaptor sequences of Pacbio Hifi reads
mergePacBioCCSreportsMerge multiple PacBio CCS report files
curationpretextA Nextflow DSL2 pipeline for pretext generation in curation
ensemblrepeatdownloadNextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure
ensemblgenedownloadNextflow pipeline to download gene annotations from Ensembl onto the Tree of Life directory structure
insdcdownloadNextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directories