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Genomes Sequence Assembly Software Links & Reviews  

2011-07-13 10:33:46|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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http://sequenceassembly.com/

Free Software

BioEdit - a very popular free sequence alignment editor for Windows.

Staden Package - a powerful open source sequence assembly and editing package for UNIX, Linux, Windows, and Mac OS X. Not the most user-friendly package, steep learning curve.

Se-Al - An older sequence alignment editor for Mac OS X. Not updated since 2002, but still popular.

4Peaks - A free trace viewer and editor for Mac OS X.

 

Commercial Software

CodonCode Aligner - A powerful sequence assembly program for Windows and Mac OS X. Free demo downloads (no forms), 30-day fully functional trial. Published prices, significantly less expensive than other popular packages.

Sequencher - Perhaps the most commonly used package in the USA. Prices for licenses are not listed at the web site, but typically start at several thousand dollars.

DNASTAR Lasergene - Another popular sequence assembly program. Similar in price to Sequencher. Trials and prices available only through web forms.

 

 

Sequence Assembly Software

This site is dedicated to software for DNA sequence assembly and alignment. Sequence assembly refers to the process of merging DNA fragments into larger "contigs" for subsequent analysis. An overview of different problems and approaches is available on Wikipedia.

Free and Open Source Sequence Assembly Programs

Gap4 / Gap5 Open source sequence assembler for Sanger sequencing. Part of the Staden package of DNA sequence analysis tools.
Phrap

The sequence assembly program Phrap was developed to assemble shotgun cosmid and BAC sequencing projects in the Human Genome Project. Phrap pioneered a number of important idea, including the automatic use of entire sequences without trimming and accurate consensus sequences based on sequence qualities and confirmation by other reads.
Free for academic research use.

Celera Assembler The program that was used to assemble the first human genome, released as open source in 2004. Assembles Sanger sequencing data and Roche 454 data.
Arachne A whole genome assembler for Sanger sequencing reads developed at the Broad Institute. BAC2BAC and fosmid Free for research and educational use.
ALLPATH A sequence assembly program for whole genome assemblies from short ("next generation") sequencing reads from MIT's Broad Institute. Free for research and educational use.
MUMmer An open source software package for aligning whole genomes.
AMOS A Modular, Open Source whole genome assembler. A collaboration of four research institutes.

Genome Assembly Benchmark Data

The Center for Bioinformatics and Computational Biology at the University of Maryland has compiled a collection of sequence data from several bacterial genomes for benchmarking sequence assembly software.


http://en.wikipedia.org/wiki/Sequence_assembly

Available assemblers

The following table lists assemblers that have a de-novo assembly capability on at least one of the supported technologies.[6]

Name Type Technologies
and

algorithm

Author Presented /

Last updated

Licence* Homepage
ABySS (large) genomes Solexa, SOLiD
 De Bruijn graph(DBG)
Simpson, J. et al. 2008 / 2011 NC-A link
ALLPATHS-LG (large) genomes Solexa, SOLiD (DBG) Gnerre, S. et al. 2011 OS link
AMOS genomes Sanger, 454 Salzberg, S. et al. 2002? / 2008? OS link
Arapan-M Medium Genomes (e.g. E.coli) All Sahli, M. & Shibuya, T. 2011 / 2012 OS link
Arapan-S Small Genomes (Viruses and Bacteria) All Sahli, M. & Shibuya, T. 2011 / 2012 OS link
Celera WGA Assembler / CABOG (large) genomes Sanger, 454, Solexa
overlap-layout-consensus(OLC)
Myers, G. et al.; Miller G. et al. 2004 / 2010 OS link
CLC Genomics Workbench & CLC Assembly Cell genomes Sanger, 454, Solexa, SOLiD
OLC
CLC bio 2008 / 2010 / 2011 C link
Cortex genomes Solexa, SOLiD Iqbal, Z. et al. 2011 OS link
DNA Baser genomes Sanger, 454 Heracle BioSoft SRL 12.2013 C www.DnaBaser.com
DNA Dragon genomes Illumina, SOLiD, Complete Genomics, 454, Sanger SequentiX 2011 C link
DNAnexus genomes Illumina, SOLiD, Complete Genomics DNAnexus 2011 C link
Edena genomes Illumina
OLC
D. Hernandez, P. Fran?ois, L. Farinelli, M. Osteras, and J. Schrenzel. 2008/2013 OS link
Euler genomes Sanger, 454 (,Solexa ?) Pevzner, P. et al. 2001 / 2006? (C / NC-A?) link
Euler-sr genomes 454, Solexa Chaisson, MJ. et al. 2008 NC-A link
Forge (large) genomes, EST, metagenomes 454, Solexa, SOLID, Sanger Platt, DM, Evers, D. 2010 OS link
Geneious genomes Sanger, 454, Solexa, Ion Torrent, Complete Genomics, PacBio, Oxford Nanopore, Illumina Biomatters Ltd 2009 / 2013 C link
Graph Constructor (large) genomes Sanger, 454, Solexa, SOLiD Convey Computer Corporation 2011 C link
IDBA (Iterative De Bruijn graph short read Assembler) (large) genomes Sanger,454,Solexa Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Francis Y. L. Chin 2010 (C / NC-A?) link
LIGR Assembler (derived from TIGR Assembler) genomic Sanger - 2009/ 2012 OS link
MaSuRCA (Maryland Super Read - Celera Assembler) (large) genomes Sanger, Illumina, 454
hybrid approach
Aleksey Zimin, Guillaume Mar?ais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke 2012 / 2013 OS link
MIRA (Mimicking Intelligent Read Assembly) genomes, ESTs Sanger, 454, Solexa Chevreux, B. 1998 / 2011 OS link
NextGENe (small genomes?) 454, Solexa, SOLiD Softgenetics 2008 C link
Newbler genomes, ESTs 454, Sanger(OLC) 454/Roche 2009 C link
PADENA genomes 454, Sanger 454/Roche 2010 OS link
PASHA (large) genomes Illumina Liu, Schmidt, Maskell 2011 OS link
Phrap genomes Sanger, 454, Solexa
(OLC)
Green, P. 1994 / 2008 C / NC-A link
TIGR Assembler genomic Sanger - 1995 / 2003 OS link
Ray[7] genomes Illumina, mix of Illumina and 454, paired or not Sébastien Boisvert, Fran?ois Laviolette & Jacques Corbeil. 2010 OS [GNU General Public License] link
Sequencher genomes traditional and next generation sequence data Gene Codes Corporation 1991 / 2009 / 2011 C link
SeqMan NGen (large) genomes, exomes, transcriptomes, metagenomes, ESTs Illumina, ABI SOLiD, Roche 454, Ion Torrent, Solexa, Sanger DNASTAR 2007 / 2011 C link
SGA (large) genomes Illumina, Sanger (Roche 454?, Ion Torrent?) Simpson, J.T. et al. 2011 / 2012 OS link
SHARCGS (small) genomes Solexa Dohm et al. 2007 / 2007 OS link
SOPRA genomes Illumina, SOLiD, Sanger, 454 Dayarian, A. et al. 2010 / 2011 OS link
SparseAssembler (large) genomes Illumina, 454, Ion torrent Ye, C. et al. 2012 / 2012 OS link
SSAKE (small) genomes Solexa (SOLiD? Helicos?) Warren, R. et al. 2007 / 2007 OS link
SOAPdenovo genomes Solexa
(DBG)
Li, R. et al. 2009 / 2009 OS link
SPAdes (small) genomes, single-cell Illumina, Solexa Bankevich, A et al. 2012 / 2013 OS link
Staden gap4 package BACs (, small genomes?) Sanger Staden et al. 1991 / 2008 OS link
Taipan (small) genomes Illumina Schmidt, B. et al. 2009 OS link
VCAKE (small) genomes Solexa (SOLiD?, Helicos?) Jeck, W. et al. 2007 / 2007 OS link
Phusion assembler (large) genomes Sanger
(OLC)
Mullikin JC, et al. 2003 OS link
Quality Value Guided SRA (QSRA) genomes Sanger, Solexa Bryant DW, et al. 2009 OS link
Velvet



(small) genomes Sanger, 454, Solexa, SOLiD
(DBG)
Zerbino, D. et al. 2007 / 2009 OS link
*Licences: OS = Open Source; C = Commercial; C / NC-A = Commercial but free for non-commercial and academics; Brackets = unclear, but most likely C / NC-A

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