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Table 1 Benchmark tests of different alignment software.

From: JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

Application RMAP SeqMap8 Maq5 SOAP6 JANE Bowtie7
Long reads (contigs)1 Running time (s) 2.2 18.2 3.2 n.a. 15.7 9.6
  No of mapped reads 107
(83.6%)
0 0 0 125
(97.7%)
0
Variable ESTs 2 Running time (s) 0.8 13.1 1.0 n.a . 8.7 3.1
  No of mapped reads 128
(41.3%)
0 0 0 154
(49.7%)
0
EST fragments (40 bp) 3 Running time (s) 0.4 7.8 1.7 2.4 8.1 3.3
  No of mapped reads 28
(9.0%)
186
(60.0%)
172
(55.5%)
172
(55.5%)
239
(77.1%)
170
(54.8%)
Shortest reads (40 bp)4 Running time (s) 0.4 7.4 1.6 2.4 7.9 3.7
  No of mapped reads 310
(100%)
310
(100%)
310
(100%)
310
(100%)
310
(100%)
310
(100%)
  1. We indicate the challenge in mapping and the distance of the template genome used for mapping. Bold: Moderate similar template genome, italics: closely-related genome template. Normal: cognate genome template.
  2. 1Long reads: 128 from a library of Staphylococcus aureus contigues (minimum lengths 627 bp or longer). Times are given in seconds. Accuracy of mapping was determined as given in materials and methods.
  3. 2Variable ESTs: 310 from a library of Blattabacteria reads with a minimum length of 19 bp.
  4. 3EST fragments trimmed to a fixed length of 40 bp.
  5. 4Short reads: 310 artificial fragments of 40 nucleotide length generated from the Blattabacteria genome sequence.
  6. 5Maq is not suitable for long reads (see Additional File 1), e.g., ESTs of variable lengths, it is customized for the Illumina-Solexa genome analyzer with a sequence limit of 63 bp.
  7. 6 n.a. not applicable for mapping long reads due to a length limit of SOAP (specialized on very short reads of 20-40 bp).
  8. 7The alignment procedure of Bowtie is remarkable faster than other software, however for a fair comparison, the time for index building has still to be included.
  9. 8SeqMap did not find one entry when aligning short reads, but this is an untypical case with long repeats, we repeated the test replacing this read, the number of mapped reads is then 100%.