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Blat can be downloaded from [1]

Aligning short reads

To compress a genome to binary database format:

 faToTwoBit ~/reference-genomes/dna/Homo_sapiens.NCBI36.52.dna.genome.fa human.reference.2bit

To search 454 against the reference and output BLAST m9 format (parsed by tissueinfo):

 blat human.reference.2bit readsfile.fasta  -ooc=11.ooc -t=dna -out=blast9

If the reads are very different from the reference, it could be useful to use shorter k-mers (i.e., 8).

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