Table 4

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 **


† 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

Kumar and Blaxter BMC Genomics 2010 11:571   doi:10.1186/1471-2164-11-571

Open Data