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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 |字号大中小订阅

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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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