I am using Bowtie2 for aligning contigs with N50 ~5Mb to a reference. I am getting the following error:
bowtie2-align died with signal 6 (ABRT) (core dumped)
I am using a machine with 100 GB RAM, and 24 cores, so I think memory should not be an issue. Is there any fix for this issue?
Alternatively, I am considering BWA-mem, BLAST, BLAT, SOAP2 and Mummer for the above task. Which one of these is most appropriate, given that I prefer an end-to-end alignment for each contig, instead of an accurate local chimeric alignment?