Table 1.
Genome sequencing and assembly
| Parameter | R. commune (UK7) | R.c. (AU2) | R.commune (13-13) | R. secalis | R. agropyri | R. ortho-sporum | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Primary seq. data | Illumina PE (GAIIx) | Illumina PE (GAIIx) | Illumina MP (GAIIx) | 454 | Illumina PE (GAIIx) | Illumina PE (GAIIx) | 454a | Illumina PE (GAIIx) | 454 | Illumina PE (GAIIx) | Illumina PE (GAIIx) | Illumina PE (HiSeq) | Illumina MP (HiSeq) | Illumina PE (GAIIx) |
| No. of reads | 18 Mio. | 35 Mio. | 6.5 Mio | 2.37 Mio | 32.1 Mio. | 25.23 Mio. | 2.21 Mio | 34.7 Mio. | 1.86 Mio. | 34 Mio. | 104 Mio. | 26 Mio. | 24 Mio. | 38 Mio. |
| Read length | 2 × 36 bp | 2 × 151 bp, 270 bp dist. | 2 × 151 bp, 3 kb dist. | 377 bp | 2 × 101 bp | 2 × 76 bp | 366.5 bp | 2 × 101 bp | 410 bp | 2 × 101 bp, 300 bp dist. | 2 × 100 bp, 180 bp dist. | 2 × 151 bp, 270 bp dist. | 2 × 151 bp, 3 kb dist. | 2 × 101 bp |
| Total length | 1.29 Gb | 9.7 Gb | 1.4 Gb | 894 Mb | 6.48 Gb | 1.92 Gb | 810 Mb | 7.0 Gb | 746 Mb | 6.9 Gb | 20.8 Gb | 7.8 Gb | 7.3 Gb | 7.6 Gb |
| Nominal seq. depth | 26x | 194x | 29x | 18x | 130x | 25x | 15x | 140x | 15x | 137x | 420x | 156x | 146x | 150x |
| Assembly software | ALLPATHS-LG + SSPACE | Velvet | Velvet + Newbler + Minimus2 | Newbler | ALLPATHS-LG + SSPACE | Velvet | ||||||||
| Total seq. length (LFI) | 55.59 Mb | 54.32 Mb | 53.93 Mb | 56.80 Mb | 52.18 Mb | 58.16 Mb | ||||||||
a 0.5 run 20 kb PE library, 1.5 runs 0.8 kb library