Repositories list

• tola-data

  Public
  Data management for the Tree of Life genome assembly pipeline

  Python

  •

  MIT License

  •1•1•0•0•Updated Aug 1, 2025Aug 1, 2025

• 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 Aug 1, 2025Aug 1, 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 Aug 1, 2025Aug 1, 2025

• tolid-api

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

  Python

  •0•0•0•3•Updated Aug 1, 2025Aug 1, 2025

• variantcalling

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

  workflowpipelinegenomics+ 3nextflowalignmentvariant-calling

  Nextflow

  •

  MIT License

  •9•8•12•2•Updated Aug 1, 2025Aug 1, 2025

• genomeassembly

  Public
  Implementation of ToL genome assembly workflows

  pipelinegenomicsnextflow+ 1genome-assembly

  Nextflow

  •

  MIT License

  •4•20•8•2•Updated Aug 1, 2025Aug 1, 2025

• treeval

  Public
  Pipelines for the production of Treeval data

  quality-controlpipelinegenomics+ 5nextflowsyntenycurationgenome-assemblygenome-alignment

  Nextflow

  •

  Other

  •5•25•36•1•Updated Aug 1, 2025Aug 1, 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 Jul 31, 2025Jul 31, 2025

• ascc

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

  genomicsnextflowpipeline

  Python

  •

  MIT License

  •0•5•18•5•Updated Jul 31, 2025Jul 31, 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

  •6•13•29•2•Updated Jul 31, 2025Jul 31, 2025

• curationpretext

  Public
  A Nextflow DSL2 pipeline for pretext generation in curation

  genomicsnextflowhic+ 1pipeline

  Nextflow

  •

  Other

  •5•10•12•0•Updated Jul 31, 2025Jul 31, 2025

• metagenomeassembly

  Public
  pipelinenextflow

  Nextflow

  •

  MIT License

  •0•2•14•1•Updated Jul 30, 2025Jul 30, 2025

• bioscan_sciops

  Public
  Script for generation of bioscan sciops manifest given a list of plate IDs

  Jupyter Notebook

  •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• PretextMap

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

  C

  •

  Other

  •3•22•7•0•Updated Jul 29, 2025Jul 29, 2025

• variantcomposition

  Public
  Nextflow

  •

  MIT License

  •1•0•8•0•Updated Jul 29, 2025Jul 29, 2025

• ear

  Public
  ERGA Assembly Report pipeline

  workflowpipelinegenomics+ 2nextflowreporting-tool

  Nextflow

  •

  MIT License

  •0•0•2•1•Updated Jul 28, 2025Jul 28, 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

  •8•26•15•2•Updated Jul 25, 2025Jul 25, 2025

• nf-core-modules

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

  nextflow

  Nextflow

  •

  MIT License

  •0•0•3•0•Updated Jul 24, 2025Jul 24, 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 Jul 24, 2025Jul 24, 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 Jul 23, 2025Jul 23, 2025

• bioscan_anospp_metadata

  Public
  Metadata handling for BIOSCAN project

  Jupyter Notebook

  •0•0•2•1•Updated Jul 22, 2025Jul 22, 2025

• nfmicrofinder

  Public
  A Pipeline to Identify Microchromosomes in a Genome Assembly

  Nextflow

  •

  MIT License

  •1•0•0•1•Updated Jul 21, 2025Jul 21, 2025

• software-tracker

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

  Python

  •

  MIT License

  •1•0•0•0•Updated Jul 18, 2025Jul 18, 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•12•1•Updated Jul 16, 2025Jul 16, 2025

• hifi-trimmer

  Public
  Python

  •

  MIT License

  •0•3•0•0•Updated Jul 9, 2025Jul 9, 2025

• TeloX

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

  Makefile

  •0•1•0•0•Updated Jul 8, 2025Jul 8, 2025

• zippypretext

  Public
  A Nextflow pipeline that generates Hi-C maps in Pretext format while preserving previous alignment information.

  workflowpipelinegenomics+ 2nextflowhic

  0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• sequencecomposition

  Public
  Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition

  pipelinegenomicsnextflow+ 3kmer-frequency-countshannon-entropyrunning-average

  Groovy

  •

  MIT License

  •2•2•20•0•Updated Jun 27, 2025Jun 27, 2025

• insdcdownload

  Public
  Nextflow DSL2 pipeline to download assemblies from INSDC.

  pipelinegenomicsnextflow+ 2downloadindexing

  Groovy

  •

  MIT License

  •2•1•6•0•Updated Jun 27, 2025Jun 27, 2025

• genealignment

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

  pipelinegenomicsnextflow+ 1gene-alignment

  Nextflow

  •

  MIT License

  •0•0•3•0•Updated Jun 27, 2025Jun 27, 2025