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/ webcite

CLC Assembly Cell 3.0

de Bruijn graph

Yes

CLC

Request quote or trial license

No

http://www.clcbio.com/ webcite

MIRA 3.0

OLC

No

Bastien Chevreux [40]

Free

Yes, GPL

http://sourceforge.net/projects/mira-assembler/ webcite

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 webcite

SeqMan NGen 2.1

OLC

No

DNAStar [41]

Request quote or trial license

No

http://www.dnastar.com/t-products-seqman-ngen.aspx webcite


* i.e. data from one read can appear in multiple contigs

† OLC: Overlap-Layout-Consensus

Kumar and Blaxter BMC Genomics 2010 11:571   doi:10.1186/1471-2164-11-571

Open Data