How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

Table 2 Available options in SOAP2, Bowtie, BWA, and Novoalign

	SOAP2 (2.20)	Bowtie (0.12.3)	BWA (0.5.8 C)	Novoalign (2.07.00)
Mismatch allowed	exactly 0,1,2	max in seed, 0-3 max in read	up to k*	up to 8 or more in single end;
Alignments reported per read	random/all/none	up to any	up to any	random/all/none/
Gap alignment	1-3 bp gap	unavailable	available	up to 7 bp
Pair-end reads	available	available	available	available
Best alignment	minimal number of mismatch	minimal number of mismatch	minimal number of mismatch	highest alignment score
Trim bases	3’ end	3’ and 5’ end	available	3’ end**

*Given a read of length m, less than 4% of m-long reads with 2% uniform base error rate may have more than k mismatches. For m = 15-37 bp, k = 2; for m = 38-64 bp, k = 3; for m = 64-92 bp, k = 4; for m = 92-123 bp, k = 5; for m = 124-156 bp, k = 6.
**only available for single-end reads.

ISSN: 1756-0381