Repositories list

• components

  Public
  UI components - this is a mirror of the internal GitLab repository. Please do not commit to this repo.

  TypeScript

  •0•0•0•0•Updated Oct 24, 2025Oct 24, 2025

• nf-core-modules

  Public
  Repository to host Tree of Life's Nextflow DSL2 modules

  nextflow

  Nextflow

  •

  MIT License

  •1•0•11•5•Updated Oct 24, 2025Oct 24, 2025

• genomeassembly

  Public
  Implementation of ToL genome assembly workflows

  pipelinegenomicsnextflow+ 1genome-assembly

  Nextflow

  •

  MIT License

  •4•23•3•2•Updated Oct 24, 2025Oct 24, 2025

• readmapping

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

  pipelinegenomicsnextflow+ 1read-alignment

  Nextflow

  •

  MIT License

  •7•13•28•1•Updated Oct 24, 2025Oct 24, 2025

• metagenomeassembly

  Public
  A Nextflow pipeline for the assembly and binning of metagenomes from PacBio HiFi and Illumina Hi-C sequencing data.

  pipelinenextflow

  Nextflow

  •

  MIT License

  •0•3•12•0•Updated Oct 24, 2025Oct 24, 2025

• PretextView

  Public
  OpenGL Powered Pretext Contact Map Viewer

  C++

  •

  Other

  •9•48•14•0•Updated Oct 24, 2025Oct 24, 2025

• ear

  Public
  ERGA Assembly Report pipeline

  workflowpipelinegenomics+ 2nextflowreporting-tool

  Nextflow

  •

  MIT License

  •1•0•3•2•Updated Oct 24, 2025Oct 24, 2025

• tol-sdk

  Public
  The Tree of Life Python SDK. This is a mirror of the GitLab repository - please don't commit to this repo.

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

• tol-portal

  Public
  ToL Portal website - this is a mirror of the internal GitLab repository. Please do not commit to this repo.

  Python

  •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

• tolqc

  Public
  ToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.

  Python

  •1•3•0•11•Updated Oct 22, 2025Oct 22, 2025

• ascc

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

  pipelinegenomicsnextflow

  Python

  •

  MIT License

  •2•5•21•2•Updated Oct 22, 2025Oct 22, 2025

• variantcalling

  Public
  Nextflow DSL2 pipeline to call variants on long read alignment.

  workflowpipelinegenomics+ 3nextflowalignmentvariant-calling

  Nextflow

  •

  MIT License

  •9•9•13•1•Updated Oct 17, 2025Oct 17, 2025

• treeval

  Public
  Pipelines for the production of Treeval data

  quality-controlpipelinegenomics+ 5nextflowsyntenycurationgenome-assemblygenome-alignment

  Nextflow

  •

  Other

  •5•28•38•1•Updated Oct 17, 2025Oct 17, 2025

• variantcomposition

  Public
  Nextflow DSL2 pipeline to analyse variants.

  workflowpipelinegenomics+ 1nextflow

  Nextflow

  •

  MIT License

  •1•0•7•0•Updated Oct 17, 2025Oct 17, 2025

• PretextMap

  Public
  Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

  C

  •

  Other

  •3•22•5•1•Updated Oct 14, 2025Oct 14, 2025

• tola-data

  Public
  Data management for the Tree of Life genome assembly pipeline

  Python

  •

  MIT License

  •1•1•0•0•Updated Oct 14, 2025Oct 14, 2025

• genomenote

  Public
  Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

  statisticspipelinegenomics+ 3nextflowpublicationshic

  Python

  •

  MIT License

  •7•26•14•2•Updated Oct 13, 2025Oct 13, 2025

• curationpretext

  Public
  A Nextflow DSL2 pipeline for pretext generation in curation

  pipelinegenomicsnextflow+ 1hic

  Nextflow

  •

  Other

  •5•13•13•0•Updated Oct 9, 2025Oct 9, 2025

• deconbedtofasta

  Public
  Using contamination.bed to produce decontaminated fasta.

  pipelinenextflow

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

• pipelines-website

  Public
  Code and files for the sanger-tol pipelines website.

  nextflow

  PHP

  •

  MIT License

  •253•2•1•12•Updated Oct 6, 2025Oct 6, 2025

• blobtoolkit

  Public
  Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.

  workflowpipelinegenomics+ 4nextflowblobtoolsdecontaminationgenomehubs

  Nextflow

  •

  MIT License

  •6•13•13•1•Updated Oct 3, 2025Oct 3, 2025

• TeloX

  Public
  Telox is a fast and robust tool designed to identify telomeric repeat motifs directly from genomic sequences.

  Rust

  •0•2•0•0•Updated Oct 2, 2025Oct 2, 2025

• agp-tpf-utils

  Public
  Code for manipulating AGP and TPF assembly files

  Python

  •

  MIT License

  •2•3•10•0•Updated Oct 1, 2025Oct 1, 2025

• nfmicrofinder

  Public
  This pipeline aids the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to the start of the genome assembly FASTA file.

  pipelinenextflow

  Nextflow

  •

  MIT License

  •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

• BIOSCAN_QC

  Public
  This script generates a BIOSCAN QC report and filters one consensus sequence per sample using output files from mBRAVE. It is designed specifically for processing the Wellcome Sanger Institute BIOSCAN data.

  HTML

  •0•1•0•0•Updated Sep 30, 2025Sep 30, 2025

• hifi-trimmer

  Public
  Python

  •

  MIT License

  •0•4•0•0•Updated Sep 26, 2025Sep 26, 2025

• software-tracker

  Public
  API and helper scripts for the pathogen software installation tracking database

  Python

  •

  MIT License

  •1•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• generate_ena_biosampleids

  Public
  Methods to generate Biosample IDs for cobionts and metagenomes using ENA API.

  Python

  •1•0•0•1•Updated Sep 12, 2025Sep 12, 2025

• bioscan_anospp_metadata

  Public
  Metadata handling for BIOSCAN project

  Jupyter Notebook

  •0•0•2•1•Updated Sep 10, 2025Sep 10, 2025

• busco_painter

  Public
  Paint chromosomes with BUSCOs

  R

  •

  MIT License

  •2•0•0•0•Updated Sep 9, 2025Sep 9, 2025