Available Assemblers
The following table lists assemblers that have a de-novo assembly capability on at least one of the supported technologies.
| 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 |
| Celera WGA Assembler / CABOG | (large) genomes | Sanger, 454, Solexa | Myers, G. et al.; Miller G. et al. | 2004 / 2010 | OS | link |
| CLC Genomics Workbench | genomes | Sanger, 454, Solexa, SOLiD | CLC bio | 2008 / 2010 | C | link |
| Cortex | genomes | Solexa, SOLiD | Iqbal, Z. et al. | 2011 | OS | link |
| DNA Baser | genomes | Sanger, 454 | Heracle BioSoft SRL | 2012 | 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. | 2008/2011 | C | 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 | Biomatters Ltd | 2009 / 2010 | 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 |
| 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 | genomes | Illumina, mix of Illumina and 454, paired or not | Sébastien Boisvert, François Laviolette & Jacques Corbeil. | 2010 | OS | 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 |
| 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 |
| 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 | 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 |
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