NextGenMap: fast and accurate read mapping in highly polymorphic genomes

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs

(2012) C. Vesely et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Advanced Methylome Analysis after Bisulfite Deep Sequencing: An Example in Arabidopsis

(2012) Huy Q. Dinh et al.   PLoS One

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS