halelab / adapt_purgehaplotigs_for_falconphase

Convert output of purge haplotigs to format compatible with FALCON-Phase

adapt_PurgeHaplotigs_for_FALCONPhase

Convert output of purge haplotigs to format compatible with FALCON-Phase

Scope

Purge haplotigs is a method for identifying haplotigs in PacBio genome assemblies, such as those generated with FALCON-Unzip. The method analyzes read coverage and sequence alignments to categorize primary contigs as haplotigs. Haplotytic primary contigs often occur when haplotype divergence is high (~5% or greater, depending on assembly parameters).

This script renames the haplotigs identified by purge haplotigs using the nomenclature of FALCON-Unzip. Repeat contigs are discarded.

This script makes the output of purge haplotigs compatible with FALCON-Phase.

Usage

renamePurgedHaplotigs.pl curated.fasta curated.haplotigs.fasta cns_h_ctg.fasta

Input

curated.fasta - curated primary contigs, output from purge haplotigs

curated.haplotigs.fasta - curated haplotigs, output from purge haplotigs, "new haplotigs"

cns_h_ctg.fasta - original haplotigs output from FALCON-Unzip

Output

curated.haplotigs.renamed.fasta - curated haplotigs renamed in Unzip haplotig style (e.g. 000123F_001)

Log of original and new names plus omitted repeat contigs is printed to stdout.

Dependencies

perl

samtools