BBMap is a global aligner and does not do any clipping by default and allows low-identity alignments. With the -slow flag, it will allow even more mismatches. Also, if you are mapping to genomic sequence (containing introns) then you need a splice-aware aligner such as BBMap rather than bwa; in that case, the gaps would be explained by introns.
BBMap is a global aligner and does not do any clipping by default and allows low-identity alignments. With the -slow flag, it will allow even more mismatches. Also, if you are mapping to genomic sequence (containing introns) then you need a splice-aware aligner such as BBMap rather than bwa; in that case, the gaps would be explained by introns.