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    55 repositories

    • agp-tpf-utils

      Public
      Code for manipulating AGP and TPF assembly files
      Python
      •
      MIT License
      •1•2•4•0•Updated Mar 11, 2025Mar 11, 2025

    • genomeassembly

      Public
      Implementation of ToL genome assembly workflows
      pipelinegenomicsnextflowgenome-assembly
      Nextflow
      •
      MIT License
      •3•20•11•3•Updated Mar 11, 2025Mar 11, 2025

    • ear

      Public
      ERGA Assembly Report pipeline
      workflowpipelinegenomicsnextflowreporting-tool
      Nextflow
      •
      MIT License
      •0•0•3•1•Updated Mar 11, 2025Mar 11, 2025

    • metagenomeassembly

      Public
      pipelinenextflow
      Nextflow
      •
      MIT License
      •0•1•12•1•Updated Mar 11, 2025Mar 11, 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 11, 2025Mar 11, 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•4•12•3•Updated Mar 11, 2025Mar 11, 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 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.
      workflowpipelinegenomicsnextflowblobtoolsdecontaminationgenomehubs
      Nextflow
      •
      MIT License
      •4•11•11•4•Updated Mar 11, 2025Mar 11, 2025

    • treeval

      Public
      Pipelines for the production of Treeval data
      quality-controlpipelinegenomicsnextflowsyntenycurationgenome-assemblygenome-alignment
      Nextflow
      •
      Other
      •5•23•37•2•Updated Mar 11, 2025Mar 11, 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 10, 2025Mar 10, 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
      genomicsnextflowhicpipeline
      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.
      pipelinegenomicsnextflowread-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.
      workflowpipelinegenomicsnextflowalignmentvariant-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.
      statisticspipelinegenomicsnextflowpublicationshic
      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
      pipelinegenomicsnextflowkmer-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