BioJulia/PairwiseMappingFormat.jl

Parser for the PAF format in bioinformatics

PairwiseMappingFormat

PairwiseMappingFormat.jl provide a parser for Pairwise Mapping Format (PAF) files. PAF is a simple, tab-delimited format created by programs such as minimap2.

To learn how to use the package, read the documentation

Example

PAFReader(open("file.paf")) do reader
    for record in reader
        if aln_identity(record) > 0.95 && record.alnlen > 2_000
            println(record.qname, " aligns well to ", record.tname)
        end
    end
end

Installation

Install PairwiseMappingFormat.jl from the julia REPL. Press ] to enter Pkg mode, and enter the following:

add PairwiseMappingFormat

Contributing

Make an issue or PR on this repository, or get in touch with the BioJulia community over at the Julia Slack or Zulip servers.