Table 2.
Genome assembly continuity and correctness using hybrid and self-correction approaches
| Organism | Corrected by | Assembly bp | Number of contigs (expected) | Number of contigs (actual) | N50 (expected) | N50 (actual) | LAP | Number of discordant bases | QV |
|---|---|---|---|---|---|---|---|---|---|
|
E. coli K12 |
Reference |
4,639,675 |
|
1 |
4,639,675 |
NA |
-9.65E + 07 |
4 |
>60 |
| |
MiSeq 100× |
4,647,253 |
1 |
2 |
|
2,367,319 |
-9.64E + 07 |
3 |
>60 |
| |
454 50× |
4,649,004 |
1 |
1 |
|
4,649,004 |
-9.64E + 07 |
3 |
>60 |
| |
CCS 25X |
4,653,267 |
1 |
1 |
|
4,653,267 |
-9.64E + 07 |
3 |
>60 |
| |
Self |
4,653,486 |
1 |
1 |
|
4,653,486 |
-9.64E + 07 |
3 |
>60 |
|
E .coli O157:H7 |
Near neighbor |
5,594,477 |
|
3 |
3,776,951 |
NA |
-3.82E + 07 |
1,282 |
36.40 |
| |
MiSeq 100× |
5,624,394 |
10 |
10 |
|
3,089,011 |
-3.66E + 07 |
4 |
>60 |
| |
454 40× |
5,613,057 |
10 |
12 |
|
927,294 |
-3.67E + 07 |
13 |
56.35 |
| |
Self |
5,611,389 |
10 |
9 |
|
4,324,437 |
-3.66E + 07 |
0 |
>60 |
|
B. trehalosi |
MiSeq 100× |
2,402,545 |
|
6 |
|
1,603,511 |
-3.28E + 07 |
1 |
>60 |
| |
454 50× |
2,413,761 |
|
4 |
|
1,051,672 |
-3.27E + 07 |
2 |
>60 |
| |
CCS 25X |
2,411,501 |
|
1 |
|
2,411,501 |
-3.27E + 07 |
0 |
>60 |
| |
Self |
2,411,068 |
|
1 |
|
2,411,068 |
-3.27E + 07 |
0 |
>60 |
|
M. haemolytica |
MiSeq 100× |
2,712,467 |
|
1 |
|
2,712,467 |
-3.31E + 07 |
0 |
>60 |
| |
CCS 25X |
2,739,949 |
|
2 |
|
2,686,992 |
-3.31E + 07 |
0 |
>60 |
| |
Self |
2,736,037 |
|
1 |
|
2,736,037 |
-3.31E + 07 |
0 |
>60 |
|
F. tularensis |
Near neighbor |
1,895,727 |
|
1 |
965,253 |
NA |
-1.33E + 07 |
113 |
42.25 |
| |
MiSeq 100× |
1,879,071 |
3 |
10 |
|
357,518 |
-1.33E + 07 |
0 |
>60 |
| |
454 50× |
1,863,947 |
3 |
15 |
|
201,203 |
-1.33E + 07 |
0 |
>60 |
| |
Self |
1,828,135 |
3 |
8 |
|
401,731 |
-1.33E + 07 |
0 |
>60 |
| |
Self (300×) |
1,877,407 |
3 |
3 |
|
573,021 |
-1.33E + 07 |
0 |
>60 |
|
S. enterica Newport |
Near neighbor |
5,007,719 |
|
2 |
4,827,641 |
NA |
-2.26E + 07 |
20 |
53.99 |
| |
MiSeq 56X |
5,027,784 |
4 |
2 |
|
4,918,796 |
-2.24E + 07 |
2 |
>60 |
| |
454 25X |
5,034,500 |
4 |
3 |
|
4,095,943 |
-2.24E + 07 |
2 |
>60 |
| |
CCS 22X |
5,030,885 |
4 |
2 |
|
4,921,886 |
-2.24E + 07 |
2 |
>60 |
| Self | 5,029,197 | 4 | 2 | 4,919,684 | -2.24E + 07 | 2 | >60 |
Organism: the genome being assembled. Corrected by: the short-read data used for correction. Assembly bp: the total number of base pairs in all contigs (only contigs containing at least 100 reads are included in all results). Number of contigs (expected): predicted number of contigs for a known reference (or near-neighbor). Number of contigs (actual): the number of contigs comprising the assembly. N50: N such that 50% of the genome is contained in contigs of length ≥N. LAP: the assembly likelihood score. A score closer to zero indicates a better assembly. Number of discordant bases: the number of SNPs and indels identified by mapping MiSeq sequences back to the assembly and recording discrepancies. Each incorrect base is counted (that is, an indel that is a deletion of two bases from the assembly counts as two in this column). QV: estimated from the number of discordant bases as . The QV can be converted to an error probability P=10^(-QV/10). Assemblies were generated by Celera Assembler [31] followed by post-processing with Quiver [32]. NA, not available.