Table 3

Comparison of Readjoiner and LEAP
RJ LEAP <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/82/mathml/M122','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/82/mathml/M122">View MathML</a> RJ LEAP <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/82/mathml/M123','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/82/mathml/M123">View MathML</a> RJ LEAP <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/82/mathml/M124','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/82/mathml/M124">View MathML</a> RJ RJ
Read set c22 c22 - c2 c2 - hg20× hg20× - hg30× hg40×
Genome size (Mbp) 34.9 34.9 - 238.2 238.2 - 2861.3 2861.3 - 2861.3 2861.3
Number of reads (M) 7.0 7.0 - 47.6 47.6 - 579.5 579.5 - 869.2 1155.3
Overall time 6 min 9 min 1.60× 53 min 1 h 36 min 1.81× 20 h 4 min 35 h 56 min 1.79× 34 h 9 min 51 h 16 min
Overall space (GB) 0.3 0.9 2.99× 2.0 4.0 1.98× 27.9 45.6 1.63× 39.8 52.0
Contigs 120712 113428 - 634403 630408 - 3239309 11662607 - 13497497 16253905
Total contigs length (Mbp) 45.7 43.1 - 292.2 280.6 - 2833.1 3642.7 - 4003.9 4281.1
Assembly N50 (Kbp) 1.6 1.6 - 3.2 3.0 - 3.0 1.4 - 1.2 0.9
Assembly NG50 (Kbp) 2.7 2.4 - 4.5 3.9 - 3.0 2.5 - 2.9 2.8
Longest contig (Kbp) 41.4 39.4 - 52.9 48.9 - 63.4 58.6 - 63.4 63.4

Results of applying Readjoiner (RJ) and LEAP to the datasets c22, c2, hg20× , hg30× , hg40× (ℓmin = 45). LEAP was not able to process hg30× and hg40× on the test machine with 64 GB RAM.

Gonnella and Kurtz

Gonnella and Kurtz BMC Bioinformatics 2012 13:82   doi:10.1186/1471-2105-13-82

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