Table 1.
Application of iCORN to prokaryotic and eukaryotic genome projects in various stages of completion
Organism | Sequence quality | Sequencing method | Genome size (Mb) | SNPs | Indels | Number rejected | Genome covered |
New mappable reads | Iterations | |
---|---|---|---|---|---|---|---|---|---|---|
Before (%) | After (%) | |||||||||
Plasmodium falciparum 3D7 | A | Capillary | 23 | 1906 | 368 | 30 | 97.20 | 97.56 | 24 698 | 6 |
Echinococcus multilocularis | B | Capillary | 110 | 5508 | 2520 | 2140 | 48.89 | 49.11 | 1 023 315 | 5 |
Leishmania major | B | Capillary | 33 | 594 | 1061 | 122 | 98.52 | 98.62 | 313 | 6 |
Leishmania infantum | B | Capillary | 32 | 2770 | 1878 | 320 | 89.26 | 89.72 | 5629 | 8 |
Plasmodium ovale | B | Capillary | 21 | 1431 | 238 | 1081 | 91.27 | 91.42 | 6368 | 4 |
Plasmodium berghei | B | 454 | 18 | 25 976 | 33 860 | 5639 | 88.65 | 95.38 | 140 788 | 7 |
Plasmodium berghei | B | Capillary | 22 | 1901 | 3818 | 538 | 97.18 | 97.48 | 23 805 | 7 |
Chlaymiadia trachomatis | B | Capillary | 1.0 | 487 | 16 | 18 | 99.86 | 99.997 | 9734 | 4 |
Clostridium difficile | B | 454 | 4.1 | 61 | 1652 | 32 | 99.30 | 99.43 | 1708 | 6 |
Streptococcus pneumoniae | B | RNAseq | 2.0 | 13 | 5 | 1 | 64.23 | 64.23 | 6 | 3 |
Streptococcus suis BM402 | A | Capillary | 2.1 | 2 | 1 | 0 | 98.84 | 98.85 | 15 | 2 |
Streptococcus suis P1_7 | A | Capillary | 2.0 | 0 | 0 | 0 | 99.7626 | 0 | 1 | |
Salmonella Dublin Strain | B | 454 | 5.0 | 13 | 45 | 18 | 96.84 | 96.85 | 207 | 7 |
Yersinia enterocolitica | B | Capillary | 5.0 | 25 | 235 | 6 | 99.96 | 99.97 | 131 796 | 3 |
Sequence quality: ‘A’ indicates manually finished and published genomes and ‘B’ indicates a draft assembly. SNPs and Indels shows the total number called between the first and last iteration. Rejected indicates the total number of changes that were rejected because they decreased the total of perfectly mapping reads at that location. Percent genome covered indicates how many bases are covered at least five times by perfectly mapping reads, before and after the correction. New mapable reads indicates the additional number of reads that could be mapped by SSAHA between the first and last iteration. Further information can be found in Supplementary Table S3.