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
| Name | m120208_071634 | m120228_192221 | m120228_210845 | Two SMRT cells | Three SMRT cells | Four SMRT cells |
| seqs amount:37077 | seqs amount:38542 | seqs amount:44794 | seqs amount:77117 | seqs amount:113284 | seqs amount:136333 | |
| seq avg len:2023.338161 | seq avg len:2322.679985 | seq avg len:2334.414140 | seq avg len:2184.208709 | seq avg len:2333.977711 | seq avg len:2386.664674 | |
| total:75.02 Mb | total:89.52 Mb | total:104.57 Mb | total:168.44 Mb | total:264.40 Mb | total:325.38 Mb | |
| depth: 16.13X | depth: 19.25X | depth: 22.49X | depth: 36.22X | depth: 56.86X | depth: 69.97X | |
| Corrected by raw data | ||||||
| seqs amount:26492 | seqs amount:34981 | seqs amount:40666 | seqs amount:63760 | seqs amount:98165 | seqs amount:118901 | |
| seq avg len:2352.489884 | seq avg len:2133.783826 | seq avg len:2124.597010 | seq avg len:2199.845561 | seq avg len:2286.482249 | seq avg len:2320.548322 | |
| total:62.32 Mb | total:74.64 Mb | total:86.40 Mb | total:140.26 Mb | total:224.45 Mb | total:275.92 Mb | |
| depth: 13.40X | depth: 16.05X | depth: 18.58X | depth: 30.16X | depth: 48.27X | depth: 59.34X | |
| Corrected by 118X | ||||||
| seqs amount:26666 | seqs amount:35199 | seqs amount:40811 | seqs amount:64201 | seqs amount:99285 | seqs amount:120296 | |
| seq avg len:2309.110290 | seq avg len:2095.143186 | seq avg len:2086.568670 | seq avg len:2150.165184 | seq avg len:2221.782394 | seq avg len:2252.656963 | |
| total:61.57 Mb | total:73.75 Mb | total:85.15 Mb | total:138.04 Mb | total:220.59 Mb | total:270.99 Mb | |
| depth: 13.24X | depth: 15.86X | depth: 18.31X | depth: 29.69X | depth: 47.44X | depth: 58.28X | |
| Corrected by 100X | ||||||
| seqs amount:25618 | seqs amount:61415 | seqs amount:95240 | seqs amount:115080 | |||
| seq avg len:2315.355024 | seq avg len:2165.060164 | seq avg len:2247.193879 | seq avg len:2283.976060 | |||
| total:59.31 Mb | total:132.97 Mb | total:214.02 Mb | total:262.84 Mb | |||
| depth: 12.76X | depth: 28.60X | depth: 46.03X | depth: 56.52X |