Fast and SNP-tolerant detection of complex variants and splicing in short reads

SNP-o-matic

(2009) Heinrich Magnus Manske et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   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

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble 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

Optimal spliced alignments of short sequence reads

(2008) F. De Bona et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

(2008) O. A. Hampton et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE