Tree of Life programme

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55 repositories

curationpretext
Public
A Nextflow DSL2 pipeline for pretext generation in curation
genomics nextflow hic pipeline
Nextflow
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Other
•5•6•12•2•Updated Mar 1, 2025Mar 1, 2025
longreadmag
Public
pipeline nextflow
Nextflow
•
MIT License
•0•1•8•0•Updated Feb 28, 2025Feb 28, 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 Feb 28, 2025Feb 28, 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•23•29•3•Updated Feb 28, 2025Feb 28, 2025
hifi-trimmer
Public
Python
•
MIT License
•0•1•0•0•Updated Feb 28, 2025Feb 28, 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 Feb 28, 2025Feb 28, 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 Feb 28, 2025Feb 28, 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
•4•11•11•4•Updated Feb 28, 2025Feb 28, 2025
PretextView
Public
OpenGL Powered Pretext Contact Map Viewer
C++
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Other
•8•34•8•0•Updated Feb 27, 2025Feb 27, 2025
agp-tpf-utils
Public
Code for manipulating AGP and TPF assembly files
Python
•
MIT License
•1•2•4•0•Updated Feb 27, 2025Feb 27, 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 Feb 25, 2025Feb 25, 2025
PretextGraph
Public
Embeds bedgraph data into Pretext contact maps.
C++
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Other
•2•0•1•0•Updated Feb 24, 2025Feb 24, 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•4•12•2•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.
pipeline genomics nextflow read-alignment
Nextflow
•
MIT License
•6•11•17•2•Updated Feb 24, 2025Feb 24, 2025
nf-core-tools
Public
Python package with helper tools for the nf-core community.
nextflow
Python
•
MIT License
•193•0•2•0•Updated Feb 21, 2025Feb 21, 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
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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
ear
Public
ERGA Assembly Report pipeline
workflow pipeline genomics nextflow reporting-tool
Nextflow
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MIT License
•0•0•1•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.
workflow pipeline genomics nextflow alignment variant-calling
Nextflow
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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.
statistics pipeline genomics nextflow publications hic
Python
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MIT License
•6•24•15•0•Updated Feb 10, 2025Feb 10, 2025
genomeassembly
Public
Implementation of ToL genome assembly workflows
pipeline genomics nextflow genome-assembly
Nextflow
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MIT License
•3•20•7•3•Updated Feb 7, 2025Feb 7, 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
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MIT License
•753•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
pipeline genomics nextflow kmer-frequency-count shannon-entropy running-average
Groovy
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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
ensemblrepeatdownload
Public
Nextflow DSL2 pipeline to download repeat annotations from Ensembl.
pipeline genomics nextflow download formatting
Groovy
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MIT License
•1•1•4•0•Updated Dec 16, 2024Dec 16, 2024