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Table 2 Benchmark test on mapping Solexa reads

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

Application Mapping reads* to chromosome 12 contig Mapping reads* to chromosome 21 contig
RMAP 27 (2.7%) 10 (1.0%)
JANE 37 (3.7%) 18 (1.8%)
SeqMap 26 (2.6%) 7 (0.7%)
SOAP 37 (3.7%) 11 (2.0%)
Bowtie 37 (3.7%) 11 (2.0%)
  1. * The total number of reads is 1000, we eliminated the incomplete or ambiguous reads in order to ensure all the programs run smoothly across the benchmark test. Both templates are Homo sapiens chromosome fragments within an acceptable length range for all the above applications (Solexa reads of 36 bp).