Table 1 |
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Results of assemblies of actual Illumina sequencing data on 3.0 GHz Xeon processor with 32 GB memory. |
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|
Organism |
Error rate (%) |
Depth |
Program |
Program version |
Program release date |
Maximum RAM used (GB) |
Run time (s) |
Genome covered (%) |
Largest contig (bp) |
N50 (bp) |
N80 (bp) |
Number of Contigs |
Runtime options |
|
|
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|
pina |
5.33 |
479 |
SSAKE |
3.2 |
2008 |
0.91 |
3463 |
79.8 |
3051 |
241 |
N/A |
24686 |
-m 16 |
|
pina |
5.33 |
479 |
VCAKE |
1.0 |
05/2007 |
0.74 |
8400 |
68.1 |
1721 |
101 |
N/A |
188778 |
-k 33 -o 34 |
|
pina |
5.33 |
479 |
VELVET |
0.6.04 |
03/2008 |
0.36 |
74 |
58.5 |
3076 |
285 |
N/A |
464 |
-min_contig_lgth 34 |
|
pina |
5.33 |
479 |
EDENA |
2.1.1 |
2008 |
0.24 |
210 |
77.8 |
3329 |
400 |
N/A |
3377 |
-c 34 |
|
pina |
5.33 |
479 |
QSRA |
06032008 |
06/2008 |
0.84 |
1553 |
93.1 |
1046 |
94 |
86 |
32473 |
-k 33 -o 34 |
|
pina |
5.33 |
479 |
QSRA* |
06032008 |
06/2008 |
0.91 |
1301 |
99.3 |
1771 |
85 |
85 |
83004 |
-k 33 -o 34 |
|
|
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|
gera03 |
5.18 |
376 |
SSAKE |
3.2 |
2008 |
0.78 |
1936 |
85.1 |
3613 |
347 |
42 |
18093 |
-m 16 |
|
gera03 |
5.18 |
376 |
VCAKE |
1.0 |
05/2007 |
0.64 |
3114 |
82.6 |
1964 |
157 |
96 |
175451 |
-k 33 -o 34 |
|
gera03 |
5.18 |
376 |
VELVET |
0.6.04 |
03/2008 |
0.32 |
55 |
60.2 |
4296 |
386 |
N/A |
311 |
-min_contig_lgth 34 |
|
gera03 |
5.18 |
376 |
EDENA |
2.1.1 |
2008 |
0.16 |
98 |
88.9 |
3285 |
535 |
41 |
1977 |
-c 34 |
|
gera03 |
5.18 |
376 |
QSRA |
06032008 |
06/2008 |
0.69 |
733 |
99.1 |
3012 |
71 |
71 |
21132 |
-k 33 -o 34 |
|
gera03 |
5.18 |
376 |
QSRA* |
06032008 |
06/2008 |
0.75 |
641 |
99.0 |
3012 |
569 |
167 |
60584 |
-k 33 -o 34 |
|
|
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|
suisp |
2.26 |
49 |
SSAKE |
3.2 |
2008 |
2.21 |
5941 |
95.8 |
6475 |
1036 |
355 |
15632 |
-m 16 |
|
suisp |
2.26 |
49 |
VCAKE |
1.0 |
05/2007 |
1.66 |
7202 |
99.0 |
11894 |
1577 |
718 |
487006 |
-k 36, -o 37 |
|
suisp |
2.26 |
49 |
VELVET |
0.6.04 |
03/2008 |
0.74 |
144 |
96.4 |
18690 |
4401 |
1992 |
1185 |
-min_contig_lgth 37 |
|
suisp |
2.26 |
49 |
EDENA |
2.1.1 |
2008 |
0.48 |
357 |
97.3 |
8829 |
1836 |
759 |
3254 |
-c 37 |
|
suisp |
2.26 |
49 |
QSRA |
06032008 |
06/2008 |
1.89 |
3329 |
96.9 |
11934 |
2432 |
259 |
18834 |
-k 36 -o 37 |
|
suisp |
2.26 |
49 |
QSRA* |
06032008 |
06/2008 |
2.18 |
3628 |
98.5 |
11934 |
2370 |
259 |
168464 |
-k 36 -o 37 |
|
|
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|
Five tests were run for each of three data sets, including SSAKE, VCAKE, VELVET, EDENA, QSRA without q-values, specified simply as QSRA in Table 1, and QSRA with q-values, specified as QSRA* in Table 1. In addition to the runtime options listed for VELVET, each VELVET run used a tile size of 19 and a coverage cutoff of 5. Only contigs were used, discarding unextended singletons, in the calculation of coverage, N50, and N80 values. Coverage values were determined though analysis of BLAT output by comparing the total number of bases in the reference genome with the number of bases uniquely "hit" by the BLAT alignments with assembled contigs. Thus, any contig which BLAT, using the default value of 90% identity, could not match to its reference genome did not contribute to coverage calculations. N50 and N80 values are equal to the largest contig in the output such that it and all contigs of greater length accounted for 50%/80% of total genome coverage. For S. suis, 43.8% of the 36 mer Illumina reads in the data set matched perfectly to the reference genome, which corresponds to an estimated average error rate per sequence base of 2.26%. |
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|
Bryant et al. BMC Bioinformatics 2009 10:69 doi:10.1186/1471-2105-10-69 |
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