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    49 repositories

    • agp-tpf-utils

      Public
      Code for manipulating AGP and TPF assembly files
      Python
      •
      MIT License
      •1•2•5•0•Updated Nov 18, 2024Nov 18, 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•11•3•Updated Nov 18, 2024Nov 18, 2024

    • treeval

      Public
      Pipelines for the production of Treeval data
      quality-controlpipelinegenomicsnextflowsyntenycurationgenome-assemblygenome-alignment
      Nextflow
      •
      Other
      •5•23•27•0•Updated Nov 15, 2024Nov 15, 2024

    • 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•14•2•Updated Nov 15, 2024Nov 15, 2024

    • ear

      Public
      ERGA Assembly Report pipeline
      workflowpipelinegenomicsnextflowreporting-tool
      Nextflow
      •
      MIT License
      •0•0•2•1•Updated Nov 14, 2024Nov 14, 2024

    • rapid-curation

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • genomeassembly

      Public
      Implementation of ToL genome assembly workflows
      pipelinegenomicsnextflowgenome-assembly
      Nextflow
      •
      MIT License
      •2•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

    • 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•14•2•Updated Nov 11, 2024Nov 11, 2024

    • bioscan_anospp_metadata

      Public
      Metadata handling for BIOSCAN project
      Jupyter Notebook
      •0•0•2•0•Updated Nov 11, 2024Nov 11, 2024

    • nf-core-tools

      Public
      Python package with helper tools for the nf-core community.
      nextflow
      Python
      •
      MIT License
      •191•0•4•2•Updated Nov 7, 2024Nov 7, 2024

    • 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
      •2•11•6•3•Updated Nov 4, 2024Nov 4, 2024

    • nf-core-website

      Public
      Code and files for the main nf-core website.
      Astro
      •
      MIT License
      •196•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • curationpretext

      Public
      A Nextflow DSL2 pipeline for pretext generation in curation
      genomicsnextflowhicpipeline
      Nextflow
      •
      Other
      •4•6•7•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•0•0•Updated Oct 23, 2024Oct 23, 2024

    • PretextGraph

      Public
      Embeds bedgraph data into Pretext contact maps.
      C++
      •
      Other
      •2•0•1•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

    • MicroFinder

      Public
      order a FASTA file by microchromosome specific genes
      Ruby
      •
      MIT License
      •1•2•0•0•Updated Oct 16, 2024Oct 16, 2024

    • Pretext-curation-tools

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

    • bioscan_sciops

      Public
      Script for generation of bioscan sciops manifest given a list of plate IDs
      Jupyter Notebook
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • pipelines-website

      Public
      Code and files for the sanger-tol pipelines website.
      nextflow
      PHP
      •
      MIT License
      •196•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 DSL2 pipeline to download assemblies from INSDC.
      pipelinegenomicsnextflowdownloadindexing
      Groovy
      •
      MIT License
      •2•1•4•0•Updated Jul 5, 2024Jul 5, 2024