PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

MOM: maximum oligonucleotide mapping

(2009) H. L. Eaves et al.   BIOINFORMATICS

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

(2009) You Jung Kim et al.   BIOINFORMATICS

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

(2008) Brian D. Ondov et al.   BIOINFORMATICS

ZOOM! Zillions of oligos mapped

(2008) H. Lin 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

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

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

(2008) H. Li et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

Hardness of optimal spaced seed design

(2007) François Nicolas et al.   JOURNAL OF COMPUTER AND SYSTEM SCIENCES