Tree of Life programme

genomenote

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.

treeval

Pipelines for the production of Treeval data

genomeassembly

Implementation of ToL genome assembly workflows

yahs

Yet another Hi-C scaffolding tool

blobtoolkit

Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.

readmapping

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

curationpretext

A Nextflow DSL2 pipeline for pretext generation in curation

ascc

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

gda

Genome Decomposition Analysis pipeline

MicroFinder

order a FASTA file by microchromosome specific genes

tolqc

ToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.

variantcalling

Nextflow DSL2 pipeline to call variants on long read alignment.

agp-tpf-utils

Code for manipulating AGP and TPF assembly files

sequencecomposition

Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition

ensemblgenedownload

Nextflow DSL2 pipeline to download gene annotations from Ensembl.

ensemblrepeatdownload

Nextflow DSL2 pipeline to download repeat annotations from Ensembl.

insdcdownload

Nextflow DSL2 pipeline to download assemblies from INSDC.

longreadmag

zippypretext

A pipeline that reuses previously generated Hi-C map data to create a new Hi-C map based on a new assembly structure.

rapid-curation

tol-submissions

ToL Submissions service. This is a mirror of the GitLab repository - please don't commit to this repo.

tolid-api

ToLID API and website. This is a mirror of the GitLab repository - please don't commit to this repo.

.github

GitHub configuration

bioscan_anospp_metadata

Metadata handling for BIOSCAN project

ear

ERGA Assembly Report pipeline

nf-core-tools

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

nf-core-website

Code and files for the main nf-core website.

Pretext-curation-tools

PretextGraph

Embeds bedgraph data into Pretext contact maps.

singularity-hpc

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