Hi everyone! Thanks so much for all your help and advice on this forum.
I am trying to find a good aligner that will help me deal with the problem I'm having. I have a few million reads that span two different (separate) sequences on the genome, the product of an insertion/translocation.
I need a tool that will help me determine the position where the read came from in sequence 1 and the position where it came from in sequence 2, as to determine the new structure in the genome.
I have done some short read alignment so far, and most of the programs I've used require a read to map from end to end to a given contiguous sequence in the reference.
However, I have recently learned that Bowtie2 can now do a local alignment approach, but I am not sure if its soft-trimming capabilities to find the best Local alignment are enough for what I need :
~75 nt of the read belong to sequence 1, and ~70nt (the remaining part of the read) corresponds to sequence 2. However, some nucleotides in the middle of the read may not align anywhere, or may correspond to duplications of sequence 1. So, as you can see, the alignment is pretty messy.
I've come across Mosaik, which I believe also does Smith-Waterman alignment, and in the BWA documentation it is stated that local alignments are performed as a way to rescue those reads that did not align on a first pass.
Do you have any input as to which of these options would be best, or if there are any other options out there that could help?