Algorithm or requirement behind Bowtie?

Question

BOWTIE maps test reads to a reference genome.

Basically it's a String comparison.

Reference String could be a million base pair made by combinations of A C T & G, also the test reads,

Now what is the criteria to call a test read as match, mutation, SPM mismatch, cigar etc

I am thinking in a perspective that, if I have to write my on BOWTIE in the language I like, what must be the test read, reference genome comparison rules I need to follow.

@H2CO3, I am talking about an executable, not the one around any body's neck. Please read b4 u write — user2458922, Jun 13 '13 at 10:34
You may gain some insight from the original Bowtie [paper](http://genomebiology.com/2009/10/3/R25). — Matt LaFave, Jun 21 '13 at 14:30

score 0 · Answer 1 · answered Oct 24 '15 at 03:11

Bowtie has two main alignment modes: -v mode and -n mode. -v mode doesn't care about quality scores while -n cares for the seeding region. Bowtie requires you to specify the maximum number of mismatches you allow and the maximum number of locations each read can map to. Bowtie2 considers gaps. BTW, the reads not only contain ACGT but also N's.

Algorithm or requirement behind Bowtie?

1 Answers1