Besides the papers available at, I'll keep posting some additional NGS data analysis papers below.


Guillaume Rizk and Dominique Lavenier, GASSST: global alignment short sequence search tool. Bioinformatics 2010 26: 2534-2540; doi:10.1093/bioinformatics/btq485.

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags. Bioinformatics 2010 26: 2501-2508; doi:10.1093/bioinformatics/btq460.

Smith AD, Xuan Z, and Zhang MQ (2008) Using quality scores and longer reads improves accuracy of solexa read mapping. BMC Bioinformatics, 9:128.

Nils Homer, Barry Merriman, and Stanley F. Nelson. BFAST: An Alignment Tool for Large Scale Genome Resequencing. PLoS One. 2009; 4 (11) : e7767.

T.W. Lam, Ruiqiang Li, Alan Tam, Simon Wong, Edward Wu, S.M. Yiu, High Throughput Short Read Alignment via Bi-directional BWT, 2009 IEEE International Conference on Bioinformatics and Biomedicine.

Korbinian Schneeberger, Jörg Hagmann, Stephan Ossowski, Norman Warthmann, Sandra Gesing, Oliver Kohlbacher, and Detlef Weigel. Simultaneous alignment of short reads against multiple genomes. Genome Biol. 2009; 10 (9) : R98.

Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, and Jörg Hackermüller. Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Comput Biol. 2009 September; 5 (9) : e1000502.

Nils Homer and Stanley F Nelson, Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA, Genome Biology 2010, 11 :R99

Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno, SHRiMP: Accurate Mapping of Short Color-space Reads, PLoS Comput Biol , Vol. 5, No. 5. (22 May 2009), e1000386.

The papers below are chosen:

Group members Papers Time
Jamiul Jahid, Mohammad Iftekharul Islam, Tanzir Musabbir

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches, BIOINFORMATICS, Vol. 25 no. 11 2009, pages 1424–1425

PatMaN: rapid alignment of short sequences to large databases, BIOINFORMATICS, Vol. 24 no. 13 2008, pages 1530–1532

Slides: [ppt] [pdf]

Oct 18
Xia Li

The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing, Bioinformatics (2009), Volume26, Issue1, Pp. 38-45.
SeqMap: mapping massive amount of oligonucleotides to the genome, Bioinformatics (2008), Volume24, Issue20, Pp. 2395-2396


Nov 1, 8:30-8:37pm
Kevin Charles and Padmavathi Paruchuri

GASSST: global alignment short sequence search tool. Bioinformatics. 2010 Oct 15;26(20):2534-40.

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags. Bioinformatics. 2010 Oct 15;26(20):2501-8.


Yunji Wang, Sree Devineni, and Zhen Gao

A Probabilistic Framework for Aligning Paired-end RNA-seq Data, Bioinformatics. 2010 Aug 15;26(16):1950-7.

Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform, Bioinformatics. 2009 Jul 15;25(14):1754-60.


Kyung Min Su, Arif Hossain

NGSView: an extensible open source editor for next-generation sequencing data, Bioinformatics, Volume26, Issue1, Pp. 125-126

Tablet – Next Generation Sequence Assembly Visualization, Bioinformatics, Volume26, Issue3, Pp. 401-402


Mario Floresmacias, Nguyen Nguyen, and Xuepo Ma Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform Li Heng and Richard Durbin

Fast and Accurate Long Read Alignment with Burrows-Wheeler Transform Li Heng and Richard Durbin


Chengwei Lei, Fang Yuan, Saleh Tamim
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies, Bioinformatics, Volume24, Issue13, Pp. i32-i40, by Hajirasouliha et. al.

PASS: a Program to Align Short Sequences, Bioinformatics. 2009 Apr 1;25(7):967-8. by Davide Campagna et al.


Husnu Saner Narman and Nihat Altiparmak

Classification of DNA sequences using Bloom filters, Bioinformatics (2010) 26 (13): 1595-1600.
Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment, Bioinformatics (2010) 26 (5): 683-686.

BLAT--The BLAST-Like Alignment Tool, Genome Research, 2002 12: 656-664


Jia Meng, Chifeng Ma and Manli Zhu

A fast hybrid short read fragment assembly algorithm, BIOINFORMATICS, Vol. 25 no. 17 2009

Optimal spliced alignments of short sequence reads, BIOINFORMATICS, Vol. 24 ECCB 2008, pages i174–i180


Badil Elhady, Michael Chan

PALMA: mRNA to genome alignments using large margin algorithms. Bioinformatics. 2007 Aug 1;23(15):1892-900.

Optimal spliced alignments of short sequence reads. Bioinformatics. 2008 Aug 15;24(16):i174-80.