ls2ga

ls2ga

Augment reference genome by structural information from split-alignment

usage

Local align contigs to reference sequence using last-split

lastdb -uNEAR -R01 db target.fa
lastal db query.fa | last-split > out.maf

Join split-alignments to a global alignment on a flat graph for each contig

ls2ga -M 32 -m 10000 -g flat.gfa -j aln.json target.fa query.fa out.maf

Transform graph and alignment in text format to in protobuf format

vg view -Fv flat.gfa > flat.vg
vg view -aJG aln.json > aln.gam

Create reference graph embedded differences in global-alignment

vg augment -i flat.vg aln.gam > aug.vg