Tree of Life programme

All

60 repositories

curationpretext
Public
A Nextflow DSL2 pipeline for pretext generation in curation
genomics nextflow hic pipeline
Nextflow
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Other
•5•10•12•1•Updated Aug 4, 2025Aug 4, 2025
tol-portal
Public
ToL Portal website - this is a mirror of the internal GitLab repository. Please do not commit to this repo.
Python
•0•0•0•0•Updated Aug 4, 2025Aug 4, 2025
ascc
Public
A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.
genomics nextflow pipeline
Python
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MIT License
•0•5•18•5•Updated Aug 4, 2025Aug 4, 2025
variantcalling
Public
Nextflow DSL2 pipeline to call variants on long read alignment.
workflow pipeline genomics nextflow alignment variant-calling
Nextflow
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MIT License
•9•8•12•2•Updated Aug 4, 2025Aug 4, 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 Aug 4, 2025Aug 4, 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.
pipeline genomics nextflow read-alignment
Nextflow
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MIT License
•6•13•29•2•Updated Aug 4, 2025Aug 4, 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
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MIT License
•0•0•0•0•Updated Aug 4, 2025Aug 4, 2025
tola-data
Public
Data management for the Tree of Life genome assembly pipeline
Python
•
MIT License
•1•1•0•0•Updated Aug 1, 2025Aug 1, 2025
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 Aug 1, 2025Aug 1, 2025
genomeassembly
Public
Implementation of ToL genome assembly workflows
pipeline genomics nextflow genome-assembly
Nextflow
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MIT License
•4•20•8•2•Updated Aug 1, 2025Aug 1, 2025
treeval
Public
Pipelines for the production of Treeval data
quality-control pipeline genomics nextflow synteny curation genome-assembly genome-alignment
Nextflow
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Other
•5•25•36•1•Updated Aug 1, 2025Aug 1, 2025
metagenomeassembly
Public
pipeline nextflow
Nextflow
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MIT License
•0•2•14•1•Updated Jul 30, 2025Jul 30, 2025
bioscan_sciops
Public
Script for generation of bioscan sciops manifest given a list of plate IDs
Jupyter Notebook
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
PretextMap
Public
Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
C
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Other
•3•22•7•0•Updated Jul 29, 2025Jul 29, 2025
variantcomposition
Public
Nextflow
•
MIT License
•1•0•8•0•Updated Jul 29, 2025Jul 29, 2025
ear
Public
ERGA Assembly Report pipeline
workflow pipeline genomics nextflow reporting-tool
Nextflow
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MIT License
•0•0•2•1•Updated Jul 28, 2025Jul 28, 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.
statistics pipeline genomics nextflow publications hic
Python
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MIT License
•8•26•15•2•Updated Jul 25, 2025Jul 25, 2025
nf-core-modules
Public
Repository to host Tree of Life's Nextflow DSL2 modules
nextflow
Nextflow
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MIT License
•0•0•3•0•Updated Jul 24, 2025Jul 24, 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 Jul 24, 2025Jul 24, 2025
BIOSCAN_QC
Public
This script generates a BIOSCAN QC report and filters one consensus sequence per sample using output files from mBRAVE. It is designed specifically for processing the Wellcome Sanger Institute BIOSCAN data.
HTML
•0•1•0•0•Updated Jul 23, 2025Jul 23, 2025
bioscan_anospp_metadata
Public
Metadata handling for BIOSCAN project
Jupyter Notebook
•0•0•2•1•Updated Jul 22, 2025Jul 22, 2025
nfmicrofinder
Public
A Pipeline to Identify Microchromosomes in a Genome Assembly
Nextflow
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MIT License
•1•0•0•1•Updated Jul 21, 2025Jul 21, 2025
software-tracker
Public
API and helper scripts for the pathogen software installation tracking database
Python
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MIT License
•1•0•0•0•Updated Jul 18, 2025Jul 18, 2025
blobtoolkit
Public
Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.
workflow pipeline genomics nextflow blobtools decontamination genomehubs
Nextflow
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MIT License
•6•13•12•1•Updated Jul 16, 2025Jul 16, 2025
hifi-trimmer
Public
Python
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MIT License
•0•3•0•0•Updated Jul 9, 2025Jul 9, 2025
TeloX
Public
Telox is a fast and robust tool designed to identify telomeric repeat motifs directly from genomic sequences.
Makefile
•0•1•0•0•Updated Jul 8, 2025Jul 8, 2025
zippypretext
Public
A Nextflow pipeline that generates Hi-C maps in Pretext format while preserving previous alignment information.
workflow pipeline genomics nextflow hic
0•0•0•0•Updated Jun 27, 2025Jun 27, 2025
sequencecomposition
Public
Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition
pipeline genomics nextflow kmer-frequency-count shannon-entropy running-average
Groovy
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MIT License
•2•2•20•0•Updated Jun 27, 2025Jun 27, 2025
insdcdownload
Public
Nextflow DSL2 pipeline to download assemblies from INSDC.
pipeline genomics nextflow download indexing
Groovy
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MIT License
•2•1•6•0•Updated Jun 27, 2025Jun 27, 2025
genealignment
Public
An NF-core pipeline to alignment genesets against a given reference genome.
pipeline genomics nextflow gene-alignment
Nextflow
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MIT License
•0•0•3•0•Updated Jun 27, 2025Jun 27, 2025