hitig

hitig

hitig: Get high quality contigs or regions (High confidence regions) by ONT/HiFi sequencing data

Main author	Jiaxin Yu (Yujiaxin419)
Co-authors	Yibin Wang (wangyibin)
	Xingtan Zhang (tangerzhang)

Examples

One command

hitig pipeline -f draft.contig.fasta -i sample.fastq.gz -n ploidy-level

step by step

• correct-alignments

mapping split reads to draft assembly and correct the alignments

hitig correct-alignments -f draft.contig.fasta -i sample.fastq.gz -t 20 -n ploidy-level

• find-chimeric

find split-alignments and idendify the chimeric contigs

hitig find-chimeric -p output.corrected.paf -l output.mapq.LIS.gtf -f draft.contig.fasta

• hcr

Identifing high confidence region.

## result is output.hcr_all.bed
hitig hcr \
    -l output.mapq.LIS.gtf \
    -sa output.mergedSplitAlign.txt \
    -d output.depth -b output.breakPos.txt \
    -f draft.contig.fasta \ 
    -p output.paf

How to use hitig results in phasing steps

1. use corrected fasta as draft.asm.fasta

cphasing mapper corrected.fasta sample.fastq.gz

2. use hcr.bed to filter the mapping results

cphasing alignments porec-intersection sample.porec.gz output.hcr_all.bed sample_hcr.porec.gz
cphasing-rs porec2pairs sample_hcr.porec.gz corrected.contigsizes -o sample_hcr.pairs.gz 

And then, use sample_hcr.porec.gz and sample_hcr.pairs.gz to run subsequence steps.