Table 1

GAGE-B assemblies versus iMetAMOS (iMA) assemblies on the R. sphaeroides dataset
Assembler GAGE-B rank GAGE-B N50 GAGE-B CN50 GAGE-B reference coverage GAGE-B #short-range GAGE-B #long-range iMA rank iMA N50 iMA CN50 iMA reference coverage iMA #short-range iMA #long-range
ABySS 5 21,441 21,307 99.64% 422 2 5 38,322 36,101 99.66% 674 0
MIRA 6 15,792 15,190 99.78% 424 15 4 52,034 46,977 99.84% 420 5
MaSuRCA 1 130,714 119,839 92.31% 532 2 1 163,762 139,231 92.95% 535 5
SGA 7 9,108 9,055 99.39% 295 0 7 3,657 3,655 91.96% 460 3
SOAPdenovo2 3 33,491 32,605 98.82% 343 1 3 87,036 65,337 99.86% 432 5
SPAdes 2 118,093 89,065 99.95% 605 1 2 118,214 81,505 99.76% 526 4
Velvet 4 23,979 23,230 99.10% 760 5 6 19,652 19,355 99.71% 1191 4

The table lists the relative ranking, assembly, and corrected N50 for each of the 7 assemblers common between GAGE-B and the iMetAMOS run using an automatically-selected k-mer. Assembly N50 was computed using the reference as the true genome size. Corrected N50 (CN50) was calculated as in GAGE [7]. The short-range errors are a sum of SNPs and short and long indels. The long-range errors are a sum of translocations, relocations, and inversions.

Koren et al.

Koren et al. BMC Bioinformatics 2014 15:126   doi:10.1186/1471-2105-15-126

Open Data