Table 3

Statistics of each assembly step
AFSFASSS AFSF + ASSS AF + SF + AS + SS
Trinity Trans-ABySS Trinity Trans-ABySS Trinity Trans-ABySS
After merginga
No. of contigs 227,879 571,835 297,319 636,921 379,837 720,131
Total Bases 217,485,766 359,411,943 267,708,300 398,478,666 298,801,419 444,024,673
N50 1,370 686 1,243 683 1,000 670
No. of contigs in N50 46,815 178,083 64,054 199,771 89,338 228,145
After deduplication
No. of contigs 165,174 152,963 179,876 138,487 191,858 128,990
Total Bases 139,479,895 117,699,005 151,369,559 104,950,724 151,376,565 94,829,611
N50 1,146 935 1,134 914 1,016 878
No. of contigs in N50 34,500 39,253 38,937 35,969 44,201 33,877
After scaffolding
No. of contigs 162,090 152,694 176,983 138,452 188,653 129,464
Total Bases 139,459,722 120,117,056 151,354,485 107,614,336 151,363,021 97,866,545
N50 1,177 960 1,161 942 1,041 907
No. of contigs in N50 33,941 39,124 38,409 35,915 43,481 33,927
Proportion of Ns 0.12% 0.13% 0.12% 0.13% 0.12% 0.13%
GC content 47.93% 48.69% 48.18% 48.76% 48.51% 48.81%

a Trinity_AFSFASSS and Trans-ABySS_AFSFASSS had not been merged.

Detail statistics can be found in Additional file 2. Contigs less than 300 bp were excluded.

Duan et al.

Duan et al. BMC Genomics 2012 13:392   doi:10.1186/1471-2164-13-392

Open Data