RazerS 3: Faster, fully sensitive read mapping

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

A novel and well-defined benchmarking method for second generation read mapping

(2011) Manuel Holtgrewe et al.   BMC BIOINFORMATICS

Hobbes: optimized gram-based methods for efficient read alignment

(2011) Athena Ahmadi et al.   NUCLEIC ACIDS RESEARCH

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH