Table 4.
Software packages, the number of loci they find in an SSR search, and the number of loci they find per mega base pair sequence in each of the four test data sets for four sequencing platforms (MiSeq, HiSeq1, HiSeq2, PacBio).
| MiSeq (ERR365834)a | HiSeq1 (ERR368422)b | HiSeq2 (ERR965681)c | PacBio (SRR1284764)d | |||||
| Software package | Total no. of loci | Loci/Mbp sequence | Total no. of loci | Loci/Mbp sequence | Total no. of loci | Loci/Mbp sequence | Total no. of loci | Loci/Mbp sequence |
| GMATo | 482,084 | 146.1 | 171,016 | 114.0 | 722,636 | 83.1 | 104,630 | 219.8 |
| MISA | 482,336 | 146.2 | 171,095 | 114.1 | 723,062 | 83.1 | 104,778 | 220.1 |
| MSATCOMMANDER | 388,663 | 117.8 | 135,168 | 90.1 | 543,610 | 62.5 | 82,588 | 173.5 |
| PAL_FINDER | 310,495 | 94.1 | 158,163 | 105.4 | 591,617 | 68.0 | 48,831 | 102.6 |
| Phobos (Geneious, STAMP) | 483,037 | 146.4 | 172,309 | 114.9 | 723,917 | 83.2 | 104,896 | 220.4 |
| SSR Locator | 481,863 | 146.0 | 170,934 | 114.0 | 722,580 | 83.1 | 104,120 | 218.7 |
a
6.6 million paired-end reads (2 × 250; 13.2 million total reads); 3.3-Gbp sequence; FASTA file: 3.9 GB.
b
10.9 million single-end reads (1 × 100); 1.5-Gbp sequence; FASTA file: 2.2 GB.
c
48.5 million paired-end reads (2 × 100; 97 million total reads); 8.7-Gbp sequence; FASTA file: 5.7 GB.
d
163,500 reads; 476-Mbp sequence; FASTA file: 445 MB.