Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements

BMC Systems Biology

Table 2 Average performance of the evaluated multiple reference-based scaffolders on the five testing datasets

Scaffolder	Sen.	Pre.	F-score	Cov.	NGA50	#Scaf.	Time
Multi-CSAR (NUCmer)	89.6	90.8	90.2	93.2	1,038,257	9	1.7
Multi-CSAR (PROmer)	89.3	90.4	89.8	92.5	1,016,308	7	6.3
Ragout	79.0	92.5	84.4	87.4	992,966	84	24.8
MeDuSa	78.2	81.9	80.0	83.3	671,001	26	3.8

The values of sensitivity (abbreviated as ‘Sen.’), precision (abbreviated as ‘Pre.’), F-score and genome coverage (abbreviated as ‘Cov.’) are displayed in percentage (%), and the size of NGA50 in base pairs (bp). The column ‘#Scaf.’ gives the number of scaffolds returned by each scaffolder and the column ‘Time’ displays the running time in minutes. The best result in each column is shown in bold

ISSN: 1752-0509