Issue is that --fragment-length is 3k by default, so if genomes (e.g. single contig phage genomes) are too short then they silently don't map. Maybe scan through the genomes to determine the shortest genome / contig, and automatically change to 500bp or something when input is short.
Issue is that --fragment-length is 3k by default, so if genomes (e.g. single contig phage genomes) are too short then they silently don't map. Maybe scan through the genomes to determine the shortest genome / contig, and automatically change to 500bp or something when input is short.