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PretextView
OpenGL Powered Pretext Contact Map Viewertreeval
Pipelines for the production of Treeval dataPretextMap
Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.genomeassembly
Implementation of ToL genome assembly workflowsblobtoolkit
Nextflow pipeline for BlobToolKit for Sanger ToL production suitereadmapping
Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.gda
Genome Decomposition Analysis pipelinetolqc
ToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.ascc
A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.variantcalling
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.tol-qc
Scripts to generate ToLQC reports for the Sanger Tree of Life programmecurationpretext
A Nextflow DSL2 pipeline for pretext generation in curationagp-tpf-utils
Code for manipulating AGP and TPF assembly filesvectorDB
adaptor sequences of Pacbio Hifi readstol-track
Tracking scripts for Sanger Tree of Life sequencing dataPretextSnapshot
Commandline image generator for Pretext contact maps.docker-images
asg-assembly-course-2021
Notes for the 2021 Aquatic Symbiosis Genomics assembly coursenf-core-pipeline
Guidelines and subworkflows for Nextflow pipeline development in Sanger ToLsequencecomposition
Nextflow pipeline to extract statistics from a genome about its sequence compositionmergePacBioCCSreports
Merge multiple PacBio CCS report fileslongreadmag
ensemblgenedownload
Nextflow pipeline to download gene annotations from Ensembl onto the Tree of Life directory structureensemblrepeatdownload
Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structureinsdcdownload
Nextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directoriesLove Open Source and this site? Check out how you can help us