There are/will be reads which can be removed prior to assembling an extended contig. While parsing magicBLAST results for aligned SRR's to flanking sequences from contigs, following reads can already be removed:
reads nested in flanking sequences
reads on the left hand side overlapping to the right
reads on the right hand side overlapping to the left
Currently, the logic is only present as snippet in the magicBLAST parser and not working in branch flank_screen. Need to rethink all possibilities to avoid removing extending reads. The usual mess with +/- alignments, right hand side and left hand side sequence.
janpb
commented
6 years ago
There are/will be reads which can be removed prior to assembling an extended contig. While parsing magicBLAST results for aligned SRR's to flanking sequences from contigs, following reads can already be removed:
Currently, the logic is only present as snippet in the magicBLAST parser and not working in branch flank_screen. Need to rethink all possibilities to avoid removing extending reads. The usual mess with +/- alignments, right hand side and left hand side sequence.