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Table 3 Varying read length using Bowtie, Maq and SOAP

From: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Length Program CPU time Wall clock time Peak virtual memory footprint (megabytes) Bowtie speed-up Reads aligned (%)
36 bp Bowtie 6 m 15 s 6 m 21 s 1,305 - 62.2
  Maq 3 h 52 m 26 s 3 h 52 m 54 s 804 36.7× 65.0
  Bowtie -v 2 4 m 55 s 5 m 00 s 1,138 - 55.0
  SOAP 16 h 44 m 3 s 18 h 1 m 38 s 13,619 216× 55.1
50 bp Bowtie 7 m 11 s 7 m 20 s 1,310 - 67.5
  Maq 2 h 39 m 56 s 2 h 40 m 9 s 804 21.8× 67.9
  Bowtie -v 2 5 m 32 s 5 m 46 s 1,138 - 56.2
  SOAP 48 h 42 m 4 s 66 h 26 m 53 s 13,619 691× 56.2
76 bp Bowtie 18 m 58 s 19 m 6 s 1,323 - 44.5
  Maq 0.7.1 4 h 45 m 7 s 4 h 45 m 17 s 1,155 14.9× 44.9
  Bowtie -v 2 7 m 35 s 7 m 40 s 1,138 - 31.7
  1. The performance of Bowtie v0.9.6, SOAP v1.10, and Maq versions v0.6.6 and v0.7.1 on the server platform when aligning 2 M untrimmed reads from the 1,000 Genome project (National Center for Biotechnology Information Short Read Archive: SRR003084 for 36 base pairs [bp], SRR003092 for 50 bp, and SRR003196 for 76 bp). For each read length, the 2 M reads were randomly sampled from the FASTQ file downloaded from the Archive such that the average per-base error rate as measured by quality values was uniform across the three sets. All reads pass through Maq's "catfilter". Maq v0.7.1 was used for the 76-bp reads because v0.6.6 does not support reads longer than 63 bp. SOAP is excluded from the 76-bp experiment because it does not support reads longer than 60 bp. Other experimental parameters are identical to those of the experiments in Table 1. CPU, central processing unit.