Table 1.
The performance comparison between major assembly tools on the F.tularensis dataset, which has a genome length of 1 892 775 bp and 6 907 220 number of 101 bp reads, using QUAST in default mode (Gurevich et al. 2013)
| Assembler | No. contigs (no. unaligned) | N50 | Largest (bp) | Total (bp) | MA | local MA | MA (bp) | GF (%) |
|---|---|---|---|---|---|---|---|---|
| Velvet | 358 (3 + 35 part) | 7377 | 39 381 | 1 762 202 | 11 | 36 | 84 965 | 92.09 |
| SOAPdenovo | 307 (3 + 31 part) | 8767 | 39 989 | 2 018 158 | 10 | 35 | 96 258 | 92.05 |
| ABySS | 96 (1 part) | 27 975 | 88 275 | 1 875 628 | 64 | 32 | 1 330 684 | 95.87 |
| SPAdes (−rr) | 102 (2 + 11 part) | 25 148 | 87 449 | 1 788 634 | 11 | 30 | 258 309 | 92.81 |
| SPAdes (+rr) | 100 (2 + 17 part) | 26 876 | 87 891 | 1 797 197 | 23 | 31 | 497 356 | 93.75 |
| IDBA | 109 (1 + 10 part) | 23 223 | 87 437 | 1 768 958 | 10 | 31 | 221 087 | 92.64 |
All statistics are based on contigs no shorter than 500 bp. N50 is defined as the length for which the collection of all contigs of that length or longer contains at least half of the sum of the lengths of all contigs and for which the collection of all contigs of that length or shorter also contains at least half of the sum of the lengths of all contigs. The no. unaligned is the number of contigs that did not align to the reference genome, or they were only partially aligned (part). Total is sum of the length of all contigs. MA is the number of (extensively) misassembled contigs. Local MA is the total number of contigs that had local misassemblies. MA (bp) is the total length of the MA contigs. GF is the genome fraction percentage, which is the fraction of genome bases that are covered by the assembly. −rr and ++rr denotes before and after repeat resolution, respectively.