Going to be using Novoalign for the first time. I searched the forum and manual but didn't find an appropriate answer to my questions:
1. Is there a way to set the number of mismatches allowed and reported, or does Novoalign report all mismatches up to a certain hard coded number?
2. Is there a way to get novoalign to output only reads that can align (i.e. don't report any NM reads), or do I have to just extract these from the output files post-alignment? It seems all reads are reported to output aligned or unaligned (like the .sam format).
I have over 700 million reads of 100 nt length, and several reference sequences of variable length, so I want to keep output file size minimal and avoid trial and error.