Table 4 |
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|
Basic assembly metrics |
||||||
|
CAP3 |
CLC |
MIRA |
Newbler 2.3 |
Newbler 2.5 |
SeqMan |
|
|
|
||||||
|
Number of contigs† |
24727 |
22746 |
35827 |
12019 |
21734 |
29969 |
|
Total Bases |
16733217 |
14875522 |
21339704 |
14456476 |
20066883 |
21355682 |
|
Number of contigs (> = 1 kbp) |
4403 |
4174 |
4770 |
6320 |
7661 |
6082 |
|
Total Bases (in contigs > = 1 kbp) |
6461079 |
6255785 |
7027775 |
10810962 |
13691429 |
9296011 |
|
Max contig length |
4011 |
4368 |
5784 |
5872 |
6228 |
6263 |
|
Mean contig length |
677 |
654 |
596 |
1203 |
923 |
713 |
|
N50 |
806 |
850 |
708 |
1487 |
1448 |
880 |
|
Number of contigs in N50 |
6533 |
5459 |
9148 |
3406 |
4649 |
7555 |
|
Reads used (SSAHA2) |
670425 |
679152 |
672036 |
616672 |
667597 |
681974 |
|
Multi-hit reads (SSAHA2) |
271648 |
118334 |
392884 |
249210 |
352887 |
322409 |
|
Reads used (CLC) |
690889 |
691818 |
696527 |
600132 |
681831 |
711726 |
|
Multi-hit reads (CLC) |
91951 |
24485 |
162365 |
213670 |
262178 |
128631 |
|
Time taken |
1 day* |
4 minutes * |
3 days * |
2 hours * |
45 minutes * |
6 hours ** |
|
|
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|
† only contigs > 100 bases were assessed * on a dual quad-core 3 GHz Xeon workstation with 32 GB RAM ** on a dual core 2.53 GHz Mac mini server with 4 GB RAM |
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|
Kumar and Blaxter BMC Genomics 2010 11:571 doi:10.1186/1471-2164-11-571 |
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