A random-permutations-based approach to fast read alignment

BMC Bioinformatics

Table 5 Real paired-end reads: search times.

Software	Search time (s)
	SRR023337 78 bp, paired	ERR009392 108 bp, paired
Bowtie -v 3	2004	2145
Bowtie -v 2	264	315
Bowtie -n 3	628	718
Bowtie2 -very-fast	650	848
Bowtie2 -fast	740	961
Bowtie2 -sensitive	978	1351
Bowtie2 -very-sensitive	1749	2576
BWA -o 0	903	2001
BWA -o 1	1707	3540
Permutations-based (report one)	345	259
Permutations-based (report more)	608	488

Each dataset contained 10⁶ pairs of reads from the fastq files obtained from the "1000 Genomes" website. Search times are reported.

ISSN: 1471-2105