This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into / account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject / sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold / (sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% / identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report.

NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' / and will be sensitive to this order.