I need some help with sequence alignment using BWA as I'm at my wits end.
Background: I've sequenced wheat DNA (note, highly repetitive) using the Illumina HiSeq 2000. I have contigs and scaffolds as assembled by the sequencing company and I have two reference genomes that should be pretty similar to my sequences. I have attempted sequence alignments of contigs and scaffolds against both reference genomes using BWA bwasw with default parameters. Note that the two reference genomes are in large scaffolds themselves.
Problem: I keep getting really bad alignments! Aligned sequences are heavily truncated in every instance, with less than half the sequence actually aligning to the reference! And if something does align, it's repetitive sequence. I have masked repetitive sequences and this alleviates the problem a little but doesn't solve the massive truncating problem. In addition, the majority of my sequence data doesn't align to anything and is clustered under "unaligned sequences".
Anyone with BWA experience or any experience with sequence alignment? I'd really appreciate a push in the right direction as this has been keeping me busy for much too long!