I would like to be able to align multi-Kb contigs of a non-assembled mammalian genome against the list of available mammalian genomic assemblies. I would like to do this locally since I have got many query sequences but I am not going to align the whole of the sequences of this genome, since I am doing this on a targeted manner. How can I do these alignments?
I thought I would concatenate all mammalian assemblies labeling the sequence regions with the species name and put them all into one big multi-fasta file. Then index it with bwa 0.6.1 and query this index file with bwasw.
Any other suggestions? Blast+? Blat?