Name |
Type |
Technologies |
Author |
Presented /
Last updated
|
Licence* |
Homepage |
ABySS |
(large) genomes |
Solexa, SOLiD |
Simpson, J. et al. |
2008 / 2011 |
NC-A |
link |
ALLPATHS-LG |
(large) genomes |
Solexa, SOLiD |
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 |
Myers, G. et al.; Miller G. et al. |
2004 / 2010 |
OS |
link |
CLC Genomics Workbench & CLC Assembly Cell |
genomes |
Sanger, 454, Solexa, SOLiD |
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 |
01.2014 |
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 |
D. Hernandez, P. François, 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 |
Aleksey Zimin, Guillaume Marçais, 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 |
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 |
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, François 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 |
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 |
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 |
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 |