Question: Best practice for aligning reads against two highly similar genomes #51
Description
I am using winnowmap to align sequencing reads against two highly similar genomes (strains of the same species). I would like to determine the best approach.
Can I concatenate the two genomes into a single reference and allow winnowmap to choose the best match, or should I create separate indexes for each genome and perform two independent alignments?
I found concatenating the genomes very useful because it allows me to very quickly see how reads "compete" and to which genome they do align best, but I am not sure if winnowmap's strategies and algorithms are adequate for this.