A comprehensive evaluation of assembly scaffolding tools

Table 1 Scaffolding tools

Scaffolder	Version	Publication date^a	Citations^b	Method	Install	Run	Read mapper	Comments
ABySS	1.3.6	27/02/2009	764^c	Graph	+	o	User’s choice
Bambus2	3.1.0^d	16/09/2011	37	Graph	-	-	User’s choice	Hard to install and run. Scripting work needed to prepare input for running scaffolding
GRASS	0.003	06/04/2012	1	Graph	-	-	BWA/NovoAlign	Hard to install and did not produce scaffolds
MIP	0.5	13/10/2011	16	Graph	o	-	User’s choice	A few dependencies required, significant work needed to prepare input files
Opera	1.2	19/09/2011	30	Graph	+	o	Bowtie/BWA
SCARPA	0.22	29/12/2012	3	Graph	+	o	User’s choice
SGA	0.9.43	07/12/2011	74^c	Graph	-	o	User’s choice	Several dependencies to install
SOAPdenovo2	r223	27/12/2012	47^c	Graph	o	-	SOAP2	Little documentation on how to run scaffolder module alone
SOPRA	1.4.6	24/06/2010	41	Graph	+	-	User’s choice	Scripting work needed to prepare input for running scaffolding
SSPACE	2 (basic)	07/12/2010	151	Greedy	+	+	Bowtie/BWA^e	Extremely easy to install and run

^aDate the article was first available online.
^bRetrieved from Google scholar 11 December 2013.
^cCitations will include general assembly, not just scaffolding.
^dBambus2 is part of the AMOS package. AMOS version 3.1.0 was used, but with latest goBambus2 script from the AMOS git repository.
^eBWA only available with a paid version of the software.

ISSN: 1474-760X