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Table 4 Summary of improvements made to the initial genome assemblies by PAGIT

From: Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples

Isolate Initial assembly statistics: No. N50 Av. (kb) Gaps closed by IMAGE ICORN Sequence corrections: SNP Indel RATT Gene annotations transferred Final assembly statistics: No. N50 Av. Size (kb) Paired reads aligning concordantly (%) Contaminant sequence NC BCT (kb)
UKH3 1902 94.7 4.9 330 210 27 3649 34 1000 268.7 9136 87.5 41.1 0.0
UKH4 2375 29.1 4.0 343 584 99 3503 110 1032 84.4 9293 93.5 40.1 14.1
UKH5 1305 29.9 7.0 437 189 61 3569 65 1006 142.4 9257 96.2 6.9 2.4
UKP2 3084 105.2 3.1 174 182 48 3600 67 1011 136.7 9164 85.1 89.6 1.6
UKP3 919 57.5 10.0 259 226 60 3546 55 1009 167.7 9224 90.2 2.0 0.0
UKP4 1966 49.3 4.8 334 170 108 3553 52 891 177.4 9222 91.0 7.3 0.7
UKP5 3830 9.7 2.4 1435 341 80 3527 47 1031 198.4 9329 88.6 31.4 14.6
UKP6 16895 40.3 0.8 274 3144 394 3565 417 1014 22.7 9471 81.2 685.7 69.5
UKP7 1158 30.2 7.8 321 185 80 3556 55 1026 168.7 9278 90.4 2.5 0.0
UKP8 1792 42.0 5.2 356 152 47 3545 63 1015 147.4 9290 93.5 37.9 24.4
  1. The assembly statistics (initial and final) include the number of scaffolds, scaffold N50 metric, scaffold mean length (Av.), and the total size of the final assembly. Gene annotations were transferred by RATT out of a total of 3805 gene annotations in the reference assembly. The “Contaminant sequence” column refers to the total length non-concordantly mapping read pairs that have been assembled separately and identified as non-cryptosporidium sequence (NC) and bacterial sequence (BCT)