Table 1.
Transcriptome assembly statistics for data contained in ASGARD V1.0
| Species | O. fasciatus | P. hawaiensis | G. bimaculatus | |
|---|---|---|---|---|
| Class, order | Insecta, Hemiptera | Malacostraca, Amphipoda | Insecta, Orthoptera | |
| No. of raw reads | 2 087 410 | 3 172 925 | 4 248 346 | |
| Mean read length | 297 | 400 | 349 | |
| No. of raw base pairs (bp) | 619 186 225 | 1 204 620 614 | 1 483 726 666 | |
| Assembler(s) used | Newbler v2.3, CAP3 | Newbler v2.5 | Newbler v2.5 | Newbler v2.5 |
| No. of reads input for assembly (percent of raw reads) | 2 041 966 (97.8) | 2 041 951 (97.8) | 3 157 373 (99.5) | 4 216 721 |
| No. of base pair input for assembly (percent of raw base pairs) | 566 097 669 (91.4) | 566 080 984 (91.4) | 1 179 544 291 (97.9) | 1 449 059 795 (97.7) |
| No. of reads used in assembly products (percent of reads input) | 1 773 450 (86.8) | 1 794 099 (87.9) | 2 625 830 (83.2) | 4 146 625 (98.3) |
| No. of base pairs assembled (percent of base pair input) | 508 738 047 (89.9) | 509 976 789 (90.1) | 1 027 860 567 (87.1) | 1 383 106 269 (95.4) |
| No. of isotigs | 21 097 | 20 985 | 35 301 | 21 512 |
| No. of isogroups | 16 617 | 16 849 | 25 735 | 16 456 |
| No. of singletons (percent assembled reads) | 178 770a (10.1) | 168 807a (9.5) | 276 564 (8.8) | 120 805 (2.9) |
| No. of CAP3 contigs | 28 143 | 29 434 | n/ab | n/a |
| Isotig N50 | 1735 | 1651 | 1510 | 2133 |
| No. of isotigs with BLAST hitsc (%) | 7219d (43.4) | 7305d (43.4e) | 10 424 (29.5%) | 11 943 (55.5) |
| No. of singletons with BLAST hits (%) | 2367f (2.8) | 2350g (2.8) | 9583 (3.5) | 10 815 (9.0) |
| No. of unique BLAST hits | 10 775 | 10 886 | 19 067 | 19 874 |
| No. of CAP3 contigs with BLAST hits (%) | 2594 (9.2) | 2642 (9.0%) | n/a | n/a |
| Mean no. of contigs per isotig | 1.9 | 1.8 | 2.1 | 1.7 |
| Mean no. of isotigs per isogroup | 1.3 | 1.2 | 1.4 | 1.2 |
| Mean coverage per base pair | 23.2 | 28.7 | 25.4 | 51.3 |
aRefers to the number of singletons produced by the Newbler v2.3 assembly. These singletons were further assembled with CAP3, resulting in CAP3 contigs and CAP3 singlets (reads still left as singletons); bCAP3 assembly of Newbler singletons was not performed for P. hawaiensis or G. bimaculatus assemblies; cBLASTx performed against the NCBI non-redundant database (nr) with E-value cutoff of e−5, unless otherwise specified; dBLASTx performed against RefSeq Protein database; ePercent isotigs with BLAST hits calculated by dividing by the number of isogroups, because in this case, only one isotig per isogroup was used for BLAST analysis; fTotal number of CAP3 singlets following CAP3 assembly of Newbler v2.3 singletons was 84 388; gTotal number of CAP3 singlets following CAP3 assembly of Newbler v2.5 singletons was 85 053.