How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

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

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

(2010) Faraz Hach et al.   NATURE METHODS

BRAT: bisulfite-treated reads analysis tool

(2009) Elena Y. Harris et al.   BIOINFORMATICS

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

(2009) Yangho Chen et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   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

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

Compressed indexing and local alignment of DNA

(2008) T. W. Lam 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

Optimal spliced alignments of short sequence reads

(2008) Fabio De Bona et al.   BMC BIOINFORMATICS

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

(2008) H. Li et al.   GENOME RESEARCH