Table 1 Comparison of ABySS and SOAPdenovo programs

ABySS

C++

< 16 Gb

87 h in 8 × 21 CPU cores (much reduced in current version)

Open source

SOAPdenovo

C

140 Gb

40 h in 32 core

Free binary

Algorithm and data structure

Pre-assembly error correction

de Bruijn graph

de Bruijn graph clean-up

Contiging

Scaffolding

Post-scaffolding process

ABySS

N/A

Distributed; can handle colour-space reads

Blunt-end, bubbles and tiny repeats

Removes and reports ambiguous edges

Implicitly, branch-bound search to tackle repeats

N/A

SOAPdenovo

Integrated

Single; nucleotide reads only

Blunt-end, bubbles, low coverage links and tiny repeats

Cuts ambiguous edges at boundaries

Explicitly, mask repeats

Gap closure by local assembly

Genome assembly paramters*

Contig N50 (bp)

Sum length of contigs

Scaftig N50 (bp)

Sum Length of scaftigs

Scaffold N50 (bp)

Sum length of scaffolds

Genome coverage

ABySS

860

2.1 Gb

1,499

2.18 Gb

Not reported

Not reported

68%

SOAPdenovo

886

2.1 Gb

> 4,000

2.37 Gb

>4,000

2.38 Gb

85%