HGAP
Hierarchical Genome Assembly Process (HGAP) was proposed in the ref (Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Meth 2013).
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DataSet1
We used all SMRT cells and randomly selected four and six SMRT cells three times for each, and access the correctness by Quast.
Randomly Selected Four SMRT cells
First Set
Random Get @m121024_100442_42178_c100389662550000001523034410251205_s1_p0
Random Get @m121024_122509_42178_c100389662550000001523034410251206_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Second Set
Random Get @m121024_122509_42178_c100389662550000001523034410251206_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0
Third Set
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121024_074656_42178_c100389662550000001523034410251204_s1_p0
Randomly Selected Six SMRT cells
First Set
Random Get @m121024_100442_42178_c100389662550000001523034410251205_s1_p0
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_074656_42178_c100389662550000001523034410251204_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0
Second Set
Random Get @m121024_074656_42178_c100389662550000001523034410251204_s1_p0
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Random Get @m121024_100442_42178_c100389662550000001523034410251205_s1_p0
Third Set
Random Get @m121023_224605_42178_c100389662550000001523034410251201_s1_p0
Random Get @m121023_202553_42178_c100389662550000001523034410251200_s1_p0
Random Get @m121024_032737_42178_c100389662550000001523034410251203_s1_p0
Random Get @m121024_122509_42178_c100389662550000001523034410251206_s1_p0
Random Get @m121024_010654_42178_c100389662550000001523034410251202_s1_p0
Random Get @m121024_144608_42178_c100389662550000001523034410251207_s1_p0
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 | 16 | 10 | 14 | 16 | 9 | 18 | 13 | |
| Largest contig | 2 198 457 | 3 4848 77 | 1 936 831 | 1 948 632 | 2 104 087 | 1 169 224 | 1 439 551 | |
| Total length | 4 808 733 | 4 706 800 | 4 705 398 | 4 745 036 | 4 741 512 | 4 814 718 | 4 749 785 | |
| N50 | 1 005 770 | 3 484 877 | 966 809 | 1 434 284 | 1 655 500 | 676 526 | 1 168 010 | |
| Misassemblies | ||||||||
| # misassemblies | 19 | 9 | 12 | 15 | 14 | 17 | 11 | |
| Misassembled contigs length | 2 939 040 | 3 530 352 | 2 949 761 | 3 653 461 | 3 820 624 | 2 387 129 | 3 986 402 | |
| Mismatches | ||||||||
| # mismatches per 100kbp | 0.8 | 0.43 | 0.58 | 1.36 | 0.15 | 0.95 | 0.58 | |
| # indels per 100kbp | 5.71 | 2.98 | 4.45 | 9.56 | 1.77 | 8.02 | 6.88 | |
| # N's per 100kbp | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| Genome Statistics | ||||||||
| Genome fraction(%) | 100 | 100 | 99.815 | 99.87 | 100 | 99.995 | 99.979 | |
| Duplication ratio | 1.037 | 1.016 | 1.017 | 1.025 | 1.022 | 1.038 | 1.025 | |
| # genes | 4494+3 part | 4494+3 part | 4480+7 part | 4485+9 part | 4494+3 part | 4493+4 part | 4492+5 part | |
| NGA50 | 615 234 | 1 205 052 | 572 342 | 875 953 | ||||
| Running Time | 19hr 06m | 13hr 34m | 13hr 21m | 12hr 38m |