Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
Figure 3
Comparison of recall rates and running time for several short read aligners.
Average running time for the different programs (A) in matching runs with 500 000 reads in two different data sets (logarithmic scale; S refers to segemehl). The differences are uniformly distributed and consist of only mismatches (B) or mismatches, insertions and deletions (C). The recall rate describes the fraction of reads which was mapped to the correct position. All programs were used with default parameters. Bowtie was called with option –all and SOAP with option –r 2.