I recently aligned (mapped to reference) some nanopore reads from Drosophila melanogaster obtained with Oxford Nanopore MINion. My reads are filtered so that only those with a quality score higher than 10 remain. I aligned the fastq file against D. melanogaster reference genome v6.32 with BWA MEM and NanoPipe, both with default parameters. When I visualized the alignments outputs (bam files) with Tablet, I found that there are some big difference regarding the coverage of some chromosomes. For example, the chromosome 3L has a complete coverage when aligned with BWA MEM, but only half coverage when aligned with NanoPipe (I attached a picture with the comparison of this alignments). Consequently, the consensus I have obtained from the alignment using NanoPipe contains wide gaps in some regions. If I use the consensus sequence obtained from the alignment using BWA MEM, I obtain more complete sequences for Drosophila`s chromosomes.
In this case, my question is, what aligner should I use ? It is more appropiate to use NanoPipe with the default parameters instead of BWA MEM, given that my reads are generated by the MINion Nanopore ?
Thank you !