Each of the commercial vendors has their own proprietary software, so we will emphasize the open source.
A great page about Next-Gen software on SeqAnswers
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Jonathan Butler, Iain MacCallum, Michael Kleber, Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, and David B. Jaffe
Genome Res. 2008 18: 810-820.
Image Processing
Basecalling
alternative base calling for 454 sequencer with improved quality scores. Developed by the Marth lab at Boston College
Open source primary data analysis for next-gen DNA sequencers
Alignment to a Reference Sequence
Maq Mapping and Assembly with Quality
Gapped alignments to reference genome, another from the Marth lab at Boston College
Novoalign from Novocraft in Kuala Lumpur, Malaysia
SOAP — Short Oligonucleotide Alignment Program
GNU Public License
from the Bioinformatics Dept of the Beijing Genomics Institute
Ruiqiang Li, et. al. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008 24: 713-714
Maps sequence reads to genomic location, variable number of mismatches and overall quality cutoff score. By Andrew D. Smith and Zhenyu Xuan in the Zhang lab at Cold Spring Harbor.
ZOOM (Zillions Of Oligos Mapped)
Product of the Michael Zhang lab at Cold Spring Harbor
Bioinformatics paper
"Zoom is freely available to non-commercial users at http://bioinfor.com/zoom"
de novo Assembly
Edena (Exact de novo Assembler)
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel.
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18:821-829.
SHARCGS (SHort read Assembler based on Robust Contig extension for Genome Sequencing)
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. SHARCGS, a fast and highly accurate short-read assembly
algorithm for de novo genomic sequencing.
ALLPATHS
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Jonathan Butler, Iain MacCallum, Michael Kleber, Ilya A. Shlyakhter, Matthew K. Belmonte, Eric S. Lander, Chad Nusbaum, and David B. Jaffe
Genome Res. 2008 18: 810-820.
SSAKE (GNU Public License, written in Perl)
The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree.René L Warren, Granger G Sutton, Steven JM Jones, Robert A Holt. 2007.
Assembling millions of short DNA sequences using SSAKE.
Bioinformatics. 23:500-501.
SNP DiscoveryAnother from the Marth Lab
Genome Viewers
Another tool from the Marth Lab
from Affymetrix & GenoViz
some IGB tips from Hunstman Cancer Inst. @ Univ of Utah
LIMS
2 comments:
Kindly post a news on your blog that Labindia GPOD is organizing a Workshop on Next-Gen Sequencing Data Analysis. More Information is available at http://labindia-gpod.blogspot.com
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