Table 2.
Features of assembly programmes compared in this study
| Assembler | Type† | Splits reads* | Author | Cost | Source available | URL |
|---|---|---|---|---|---|---|
| CAP3 | OLC† | No | X Huang and A Madan [38] | Free for use at non-profit organizations | No | http://seq.cs.iastate.edu/ |
| CLC Assembly Cell 3.0 | de Bruijn graph | Yes | CLC | Request quote or trial license | No | http://www.clcbio.com/ |
| MIRA 3.0 | OLC | No | Bastien Chevreux [40] | Free | Yes, GPL | http://sourceforge.net/projects/mira-assembler/ |
| Newbler 2.3 and Newbler 2.5 | OLC | Yes | Roche 454 [37] | Free for academic use | No | http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp |
| SeqMan NGen 2.1 | OLC | No | DNAStar [41] | Request quote or trial license | No | http://www.dnastar.com/t-products-seqman-ngen.aspx |
* i.e. data from one read can appear in multiple contigs
† OLC: Overlap-Layout-Consensus