README.md

ortholint

A nextflow pipeline that creates (or takes) orthologous groups from gene-called genomes and runs sequence- and structure based QC to remove outliers

vision

setup

You have to define your own dependency profile in nextflow.config unless you have access to the VUB-HPC. Use docker/apptainer to make your life easier.

Install requirements

• Nextflow

• Singularity/Apptainer or Docker

• Copy of this repository

• Orthofinder in GitHub, or Docker

• CD-Hit eg. GitHub

• Biopython

• BLAST (V2.14)

• Pandas

• ESMfold GitHub

• Foldseek GitHub, or Docker

• Copy of SIMSApiper repository

• IQ-TREE eg. GitHub

parameters

--data "$launchDir/data"
--outFolder "$launchDir/"
--structures false [path/to/structure/dir]
--predictRemaining false
--orthoGroupSeqs [path/to/ogseqs/dir]
--minCoverage 0.8
--outGroup false [str_with_og_name]
--foldseekClusters false