Tools for mapping high-throughput sequencing data

Abstract Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial. Results: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem. Availability: A regularly updated compendium of mappers can be found at http: //wwwdev. ebi. ac. uk/fg/htsₘappers/. Contact: nf@ebi. ac. uk Supplementary information: Supplementary data are available at Bioinformatics online.