Although BWA is a very popular and well tested aligner, it’s hardly the only aligner around. There is an extensive list of open source and commercial short read aligners available on Wikipedia. Another collection can be found on the EBI webpage (there’s also information about the number of citations for each aligner on this page). SeqAnswers has a software collection page as well.

This week I will try two of the most cited (and also oldest) aligners: Bowtie and MAQ.

Bowtie (webpage, manual, tutorial, download, article)

Similarly to BWA, Bowtie needs an indexed reference for the alignment. There are some pre-built indexes available, but let’s build a new one!

$bowtie-build NC_000913.2.fa e_coli_MG1655

Then, we can run the alignment:

$bowtie -k 3 -v 3 --sam e_coli_MG1655 reads/SRR515927.fastq > alignments/SRR515927_bowtie.sam

Bowtie has two alignment modes “-n” and “-v”. The “-n” alignment mode uses the number of mismatches at the beginning of the read and the quality of mismatches in the whole read, while the “-v” mode uses the total number of mismatches in a read. Note, that like BWA, Bowtie was designed for “short-short” (less than 50bp long) reads, for today’s longer reads, Bowtie 2 is probably more suitable.

MAQ (webpage, manual, download)

MAQ is a kind of a “predecessor” of BWA and Samtools (all three have been developed by Heng Li). MAQ has been written for (again) “short short” Illumina data and it’s not just an aligner, but a consensus/variant caller as well.

$ ./maq.pl easyrun -d . ../NC_000913.2.fa ../reads/SRR022913_1.fastq ../reads/SRR022913_2.fastq

MAQ is so old, that it actually pre-dates the SAM format. Luckily, Samtools has a “maq to sam” converter:

maq2sam-long all.map > SRR022913_MAQ.sam