SCA

Revision as of 20 January 2014 20:40 by admin (Comments | Contribs) | (→DataSet1)

Self-correction approach (SCA) was proposed in the ref (Reducing assembly complexity of microbial genomes with single-molecule sequencin, Genome Biology 2013).

Contents

DataSet1

We used all SMRT cells and randomly selected four and six SMRT cells three times for each, and access the correctness by Quast.


Performance

Statistics without reference All Data 4 SMRT cells : 1st Set 4 SMRT cells : 2nd Set 4 SMRT cells : 3rd Set 6 SMRT cells : 1st Set 6 SMRT cells : 2nd Set 6 SMRT cells : 3rd Set
# contigs 2 8 10 14 1 1 4
Largest contig 4 278 957 2 277 010 1 213 670 984 459 4 641 350 4 640 250 3 162 440
Total length 4 650 771 4 648 304 4 644 602 4 656 274 4 641 350 4 640 250 4 653 394
N50 4 278 957 2 043 590 2 044 147 2 135 225 3 162 440 4 640 250 4 641 350
Misassemblies
# misassemblies 8 10 8 6 7 7 8
Misassembled contigs length 4 278 957 2 809 129 2 085 482 1 947 163 4 641 350 4 640 250 3 209 090
Mismatches
# mismatches per 100kbp 0.37 2.49 1.88 5.38 0.69 0.67 0.86
# indels per 100kbp 3.64 56.81 47.62 77.31 10.67 12.87 11
# N's per 100kbp 0 0.04 0.02 0.09 0 0 0
Genome Statistics
Genome fraction(%) 99.93 99.733 99.67 99.693 99.972 99.946 99.968
Duplication ratio 1.003 1.006 1.005 1.008 1.001 1.001 1.005
# genes 4492+5 part 4475+10 part 4467+12 part 4469+13 part 4492+4 part 4491+4 part 4492+4 part
NGA50 1 207 233 531 351 721 189 565 251 2 499 057 2 499 697 1 267 262
Running Time 15hr 41m 7hr 32m 7hr 10m 5hr 42m 15hr 44m 16hr 02m 13hr 27m

DataSet2

We used all SMRT cells to do assembly and access the correctness by Quast.

Performance

Statistics without reference All Data
# contigs 2
Largest contig 2 974 307
Total length 3 100 289
N50 2 974 307
Misassemblies
# misassemblies 3
Misassembled contigs length 2 974 307
Mismatches
# mismatches per 100kbp 0.23
# indels per 100kbp 5.04
# N's per 100kbp 0.03
Genome Statistics
Genome fraction(%) 99.883
Duplication ratio 1.002
# genes 3093+4 part
NGA50 1 715 029
Running Time ?hr ?m