The following Table enables a comparison of mappers based on different characteristics. The table can be sorted by column (just click on the column name). The data was collected from different sources and in some cases was provided by the developers. For execution times and memory requirements we refer to the above mentioned review (supplementary data is available here).
The Data column indicates if the mapper is specifically tailored for DNA, RNA, miRNA, or bisulfite sequences.The Seq.Plat. column indicates if the mapper supports natively reads from a specific sequencing platform or not (N). The version column indicates the version of the mapper considered. Read length limits are showed in two columns: minimum read length (Min. RL) and maximum read length (Max. RL.). Unless otherwise stated the unit is base pairs. The support for mismatches and short indels is also presented including, when possible, the maximum number of allowed mismatches and indels: by default the value is presented in bases; in some cases the value is presented as a percentage of the read size; or as score, meaning that mapper uses a score function. The alignments reported column indicate the alignments reported when a read maps to multiple locations. The alignment column indicates if the reads are aligned end-to-end (Globally) or not (Locally). The Parallel column indicates if the mapper can be run in parallel and, if yes, how: using a shared-memory (SM) or/and a distributed memory (DM) computer. The QA (quality awareness) column indicates if the mapper uses read quality information during the mapping. The support for paired-end/mate-pair reads is indicated in the PE column. The Splicing column indicates, for the RNA mappers, if the detection of splice junctions is made de novo or/and through user provided libraries (Lib). The Index column indicates if the reads or/and the reference are indexed. The number of citations was obtained from Google Scholar on 13 June 2015.