Table 2

Assembly metricsa
First assembly a Second assembly b
Method TGICL Newbler PAVE Iterative assembly procedure
Input datasets Sanger, 454/Roche Sanger, 454/Roche Sanger, 454/Roche PAVE contigs, Solexa/Illumina
Number of contigs (≥ 300 bp) 134,225 141,973 118,795 213,621
Total length of contigs (≥ 300 bp) 85.1 Mb 78.1 Mb 86.9 Mb 252.9 Mb
Average length of contigs 634 bp 549 bp 731 bp 1,183 bp
Median length of contigs 474 bp 434 bp 495 bp 676 bp
Maximum length of contigs 9,221 bp 7,841 bp 9,241 bp 64,116 bp
Number of large contigs (≥ 1 kb) 15,516 11,756 23,534 79,035
Total length of large contigs 24.9 Mb 19.1 Mb 38.3 Mb 183.0 Mb

a ‘First assembly’ shows the results of three assembly programs that were tested using Sanger and 454/Roche data. PAVE produced the best assembly with respect to total length, number of contigs and average contig length. b ‘Second assembly’: Solexa/Illumina data were assembled onto a backbone of PAVE contigs using an iterative assembly procedure outlined in Methods.

Petzold et al.

Petzold et al. BMC Genomics 2013 14:185   doi:10.1186/1471-2164-14-185

Open Data