Repositories list

• rapid-curation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• genomeassembly

  Public
  Implementation of ToL genome assembly workflows

  pipelinegenomicsnextflow+ 1genome-assembly

  Nextflow

  •

  MIT License

  •2•20•7•2•Updated Nov 5, 2024Nov 5, 2024

• agp-tpf-utils

  Public
  Code for manipulating AGP and TPF assembly files

  Python

  •

  MIT License

  •1•2•3•0•Updated Nov 4, 2024Nov 4, 2024

• genomenote

  Public
  This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

  statisticspipelinegenomics+ 3nextflowpublicationshic

  Python

  •

  MIT License

  •6•24•14•0•Updated Nov 4, 2024Nov 4, 2024

• blobtoolkit

  Public
  Nextflow pipeline for BlobToolKit for Sanger ToL production suite

  workflowgenomicsnextflow+ 4blobtoolsdecontaminationgenomehubspipeline

  Nextflow

  •

  MIT License

  •2•11•5•2•Updated Nov 4, 2024Nov 4, 2024

• nf-core-tools

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

  nextflow

  Python

  •

  MIT License

  •190•0•4•2•Updated Oct 29, 2024Oct 29, 2024

• nf-core-website

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

  Astro

  •

  MIT License

  •193•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• 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•10•14•2•Updated Oct 24, 2024Oct 24, 2024

• curationpretext

  Public
  A Nextflow DSL2 pipeline for pretext generation in curation

  genomicsnextflowhic+ 1pipeline

  Nextflow

  •

  Other

  •4•5•6•1•Updated Oct 24, 2024Oct 24, 2024

• yahs

  Public
  Yet another Hi-C scaffolding tool

  C

  •

  MIT License

  •19•19•0•0•Updated Oct 23, 2024Oct 23, 2024

• singularity-hpc

  Public
  Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.

  Python

  •

  Mozilla Public License 2.0

  •26•0•1•0•Updated Oct 23, 2024Oct 23, 2024

• PretextGraph

  Public
  Embeds bedgraph data into Pretext contact maps.

  C++

  •

  Other

  •2•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• 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•0•Updated Oct 21, 2024Oct 21, 2024

• ear

  Public
  ERGA Assembly Report pipeline

  workflowpipelinegenomics+ 2nextflowreporting-tool

  Nextflow

  •

  MIT License

  •0•0•1•0•Updated Oct 21, 2024Oct 21, 2024

• ascc

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

  genomicsnextflowpipeline

  Python

  •

  MIT License

  •0•3•10•1•Updated Oct 17, 2024Oct 17, 2024

• MicroFinder

  Public
  order a FASTA file by microchromosome specific genes

  Ruby

  •

  MIT License

  •1•2•0•0•Updated Oct 16, 2024Oct 16, 2024

• gda

  Public
  Genome Decomposition Analysis pipeline

  nextflow

  Python

  •

  MIT License

  •1•4•1•1•Updated Oct 12, 2024Oct 12, 2024

• Pretext-curation-tools

  Public
  0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

• treeval

  Public
  Pipelines for the production of Treeval data

  quality-controlpipelinegenomics+ 5nextflowsyntenycurationgenome-assemblygenome-alignment

  Nextflow

  •

  Other

  •4•22•32•3•Updated Oct 10, 2024Oct 10, 2024

• 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 10, 2024Oct 10, 2024

• .github

  Public
  GitHub configuration

  MIT License

  •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

• 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 Oct 7, 2024Oct 7, 2024

• 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 Oct 2, 2024Oct 2, 2024

• pipelines-website

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

  nextflow

  PHP

  •

  MIT License

  •193•1•0•11•Updated Sep 26, 2024Sep 26, 2024

• summary-stats-analyses

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• PretextView

  Public
  OpenGL Powered Pretext Contact Map Viewer

  C

  •

  Other

  •8•29•8•2•Updated Sep 19, 2024Sep 19, 2024

• software-tracker

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

  Python

  •

  MIT License

  •1•0•0•0•Updated Jul 15, 2024Jul 15, 2024

• insdcdownload

  Public
  Nextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directories

  pipelinegenomicsnextflow+ 2downloadindexing

  Groovy

  •

  MIT License

  •2•1•4•0•Updated Jul 5, 2024Jul 5, 2024

• 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 Jul 4, 2024Jul 4, 2024

• ensemblrepeatdownload

  Public
  Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure

  pipelinegenomicsnextflow+ 2downloadformatting

  Groovy

  •

  MIT License

  •0•1•3•0•Updated Jul 2, 2024Jul 2, 2024