README.md

nf-busco_phylogenomics

Introduction

nf-busco_phylogenomics is a Nextflow pipeline to build phylogenomic tree from BUSCO outputs

Usage

First, prepare a samplesheet with your input data that looks as follows:

sample.csv:

sample,fasta
species_1,species_1_genome.fasta

Each row represents a fasta file.

Now, you can run the pipeline using:

nextflow run ASUQ/busco_phylogenomics \
   -profile <docker/singularity/gwdg/oist/...> \
   --sample sample.csv \
   --lineage <busco_lineage> \
   --outdir <OUTDIR>

--fraction accepts exact decimal values such as 0.999. When the percentage is not an integer, output labels use p in place of the decimal point, for example 0.999 -> frac99p9pct_results.