Improving read mapping using additional prefix grams

RazerS 3: Faster, fully sensitive read mapping

(2012) David Weese et al.   BIOINFORMATICS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

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

AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization

(2011) Daniel Newkirk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

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

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

(2009) Can Alkan et al.   NATURE GENETICS