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Table 3 Real single-end reads: search time

From: A random-permutations-based approach to fast read alignment

Software Search time (s)
  SRR023337_1
78 bp
ERR009392_1
108 bp
ERR016249_1
160 bp
Bowtie -v 3 233 256 773
Bowtie -n 2 144 334 1560
Bowtie -n 2 -k 10 658 1142 2830
Bowtie2 -very-fast 179 285 440
Bowtie2 -sensitive 328 654 853
Bowtie2 -very-sensitive 812 1488 1855
Bowtie2 -very-sensitive -k 10 1121 2430 3869
BWA -o 0 548 860 2434
Permutations-based (mode 1) 65 68 111
Permutations-based (mode 2) 147 151 145
Permutations-based (fast) 35 39 57
  1. Each dataset contained 106 reads from the fastq files obtained from the "1000 Genomes" project.