Repositories list

• ascc

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

  genomicsnextflowpipeline

  Python

  •

  MIT License

  •0•4•12•3•Updated Mar 12, 2025Mar 12, 2025

• metagenomeassembly

  Public
  pipelinenextflow

  Nextflow

  •

  MIT License

  •0•1•12•1•Updated Mar 12, 2025Mar 12, 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 Mar 12, 2025Mar 12, 2025

• treeval

  Public
  Pipelines for the production of Treeval data

  quality-controlpipelinegenomics+ 5nextflowsyntenycurationgenome-assemblygenome-alignment

  Nextflow

  •

  Other

  •5•23•29•2•Updated Mar 12, 2025Mar 12, 2025

• tol-portal

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

  TypeScript

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 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 Mar 12, 2025Mar 12, 2025

• agp-tpf-utils

  Public
  Code for manipulating AGP and TPF assembly files

  Python

  •

  MIT License

  •1•2•2•0•Updated Mar 12, 2025Mar 12, 2025

• genomeassembly

  Public
  Implementation of ToL genome assembly workflows

  pipelinegenomicsnextflow+ 1genome-assembly

  Nextflow

  •

  MIT License

  •3•20•11•3•Updated Mar 11, 2025Mar 11, 2025

• ear

  Public
  ERGA Assembly Report pipeline

  workflowpipelinegenomics+ 2nextflowreporting-tool

  Nextflow

  •

  MIT License

  •0•0•3•1•Updated Mar 11, 2025Mar 11, 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

  •4•11•13•4•Updated Mar 11, 2025Mar 11, 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 Mar 10, 2025Mar 10, 2025

• nf-core-tools

  Public
  Python package with helper tools for the nf-core community.

  nextflow

  Python

  •

  MIT License

  •196•0•2•0•Updated Mar 7, 2025Mar 7, 2025

• curationpretext

  Public
  A Nextflow DSL2 pipeline for pretext generation in curation

  genomicsnextflowhic+ 1pipeline

  Nextflow

  •

  Other

  •5•6•14•0•Updated Mar 6, 2025Mar 6, 2025

• .github

  Public
  GitHub configuration

  MIT License

  •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• hifi-trimmer

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Feb 28, 2025Feb 28, 2025

• PretextView

  Public
  OpenGL Powered Pretext Contact Map Viewer

  C++

  •

  Other

  •8•33•9•0•Updated Feb 27, 2025Feb 27, 2025

• PretextGraph

  Public
  Embeds bedgraph data into Pretext contact maps.

  C++

  •

  Other

  •2•0•1•0•Updated Feb 24, 2025Feb 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

  •6•11•18•2•Updated Feb 24, 2025Feb 24, 2025

• TOGA

  Public
  TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

  Python

  •

  MIT License

  •23•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• generate_ena_biosampleids

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

  Python

  •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• bioscan_sciops

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

  Jupyter Notebook

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• variantcalling

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

  workflowpipelinegenomics+ 3nextflowalignmentvariant-calling

  Nextflow

  •

  MIT License

  •3•4•17•0•Updated Feb 11, 2025Feb 11, 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

  •6•24•15•0•Updated Feb 10, 2025Feb 10, 2025

• rapid-curation

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• nf-core-modules

  Public
  Repository to host Tree of Life's Nextflow DSL2 modules, alongside nf-core's

  nextflow

  Nextflow

  •

  MIT License

  •754•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• zippypretext

  Public
  A pipeline that reuses previously generated Hi-C map data to create a new Hi-C map based on a new assembly structure.

  MIT License

  •0•1•0•2•Updated Jan 21, 2025Jan 21, 2025

• tol-submissions

  Public
  ToL Submissions service. This is a mirror of the GitLab repository - please don't commit to this repo.

  Python

  •0•0•0•3•Updated Jan 20, 2025Jan 20, 2025

• variantcomposition

  Public
  1•0•0•0•Updated Jan 16, 2025Jan 16, 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

  •1•2•20•0•Updated Jan 15, 2025Jan 15, 2025

• bioscan_anospp_metadata

  Public
  Metadata handling for BIOSCAN project

  Jupyter Notebook

  •0•0•2•0•Updated Jan 7, 2025Jan 7, 2025