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Table 2 Features of assembly programmes compared in this study

From: Comparing de novo assemblers for 454 transcriptome data

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

  1. * i.e. data from one read can appear in multiple contigs
  2. † OLC: Overlap-Layout-Consensus