Convert output of purge haplotigs to format compatible with FALCON-Phase
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.
renamePurgedHaplotigs.pl curated.fasta curated.haplotigs.fasta cns_h_ctg.fasta
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
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.
perl
samtools