Repositories list

• ascc

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

  genomicsnextflowpipeline

  Nextflow

  •

  MIT License

  •0•4•7•3•Updated Jan 27, 2025Jan 27, 2025

• treeval

  Public
  Pipelines for the production of Treeval data

  quality-controlpipelinegenomics+ 5nextflowsyntenycurationgenome-assemblygenome-alignment

  Nextflow

  •

  Other

  •5•23•24•1•Updated Jan 27, 2025Jan 27, 2025

• components

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

  MIT License

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 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.

  MIT License

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• longreadmag

  Public
  pipelinenextflow

  Nextflow

  •

  MIT License

  •0•1•8•1•Updated Jan 24, 2025Jan 24, 2025

• PretextView

  Public
  OpenGL Powered Pretext Contact Map Viewer

  C++

  •

  Other

  •8•31•8•2•Updated Jan 23, 2025Jan 23, 2025

• rapid-curation

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• nf-core-modules

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

  nextflow

  Nextflow

  •

  MIT License

  •745•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• variantcalling

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

  workflowpipelinegenomics+ 3nextflowalignmentvariant-calling

  Nextflow

  •

  MIT License

  •3•4•17•0•Updated Jan 22, 2025Jan 22, 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

• ear

  Public
  ERGA Assembly Report pipeline

  workflowpipelinegenomics+ 2nextflowreporting-tool

  Nextflow

  •

  MIT License

  •0•0•2•0•Updated Jan 15, 2025Jan 15, 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•14•2•Updated Jan 15, 2025Jan 15, 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

• 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•13•0•Updated Jan 13, 2025Jan 13, 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 Jan 13, 2025Jan 13, 2025

• curationpretext

  Public
  A Nextflow DSL2 pipeline for pretext generation in curation

  genomicsnextflowhic+ 1pipeline

  Nextflow

  •

  Other

  •4•6•8•0•Updated Jan 9, 2025Jan 9, 2025

• bioscan_anospp_metadata

  Public
  Metadata handling for BIOSCAN project

  Jupyter Notebook

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

• nf-core-tools

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

  nextflow

  Python

  •

  MIT License

  •192•0•2•0•Updated Dec 16, 2024Dec 16, 2024

• ensemblrepeatdownload

  Public
  Nextflow DSL2 pipeline to download repeat annotations from Ensembl.

  pipelinegenomicsnextflow+ 2downloadformatting

  Groovy

  •

  MIT License

  •1•1•3•0•Updated Dec 16, 2024Dec 16, 2024

• ensemblgenedownload

  Public
  Nextflow DSL2 pipeline to download gene annotations from Ensembl.

  pipelinegenomicsnextflow+ 3downloadindexinggene-annotation

  Groovy

  •

  MIT License

  •2•1•4•0•Updated Dec 16, 2024Dec 16, 2024

• insdcdownload

  Public
  Nextflow DSL2 pipeline to download assemblies from INSDC.

  pipelinegenomicsnextflow+ 2downloadindexing

  Groovy

  •

  MIT License

  •2•1•4•0•Updated Dec 16, 2024Dec 16, 2024

• 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•6•1•Updated Dec 16, 2024Dec 16, 2024

• nf-core-website

  Public
  Code and files for the main nf-core website.

  Astro

  •

  MIT License

  •208•0•0•0•Updated Dec 1, 2024Dec 1, 2024

• agp-tpf-utils

  Public
  Code for manipulating AGP and TPF assembly files

  Python

  •

  MIT License

  •1•2•4•0•Updated Nov 29, 2024Nov 29, 2024

• MicroFinder

  Public
  order a FASTA file by microchromosome specific genes

  Ruby

  •

  MIT License

  •2•3•0•0•Updated Nov 21, 2024Nov 21, 2024

• genomeassembly

  Public
  Implementation of ToL genome assembly workflows

  pipelinegenomicsnextflow+ 1genome-assembly

  Nextflow

  •

  MIT License

  •3•20•7•2•Updated Nov 13, 2024Nov 13, 2024

• gda

  Public
  Genome Decomposition Analysis pipeline

  nextflow

  Python

  •

  MIT License

  •1•4•1•0•Updated Nov 12, 2024Nov 12, 2024

• yahs

  Public
  Yet another Hi-C scaffolding tool

  C

  •

  MIT License

  •20•18•0•0•Updated Oct 23, 2024Oct 23, 2024