paf2chain

convert PAF format to CHAIN format

citation

installation

paf2chain is built with rust, and so we install using cargo:

git clone https://github.com/AndreaGuarracino/paf2chain
cd paf2chain
cargo install --force --path .

usage

Generate alignments with the cigar string attached to the cg:Z: tag. These can be made by several aligners, including minimap2 -c, wfmash, or lastz --format=paf:wfmash. With alignments in aln.paf (or aln.paf.gz if gzip-compressed), we would convert it into a CHAIN format file using this call:

paf2chain -i aln.paf > aln.chain

info

paf2chain performs the reverse operation of chain2paf.