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purge-haplotigs-nf

Nextflow workflow for purging haplotigs from a genome assembly

Introduction

This pipeline uses the program purge_haplotigs to purge haplotigs from an assembly of a diploid organism.

Requirements

Only nextflow and conda or mamba are required.

Running

First, perform the alignment and create the histogram:

nextflow run WarrenLab/purge-haplotigs-nf \
    --assembly contigs.fa --subreads subreads.bam

Then, examine the histogram in histogram/ to choose low, mid, and high cutoffs, as explained in the README for purge_haplotigs. Enter those cutoffs to run the purging part of the pipeline:

nextflow run WarrenLab/purge-haplotigs-nf \
    --assembly contigs.fa --low 5 --mid 20 --high 50

Your curated assembly will now be in purged/curated.fa.