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Benchmarks: File Sizes
Simon Harris edited this page Sep 6, 2018
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Species | Accession Number | Number of Contigs | Genome Length | File size |
---|---|---|---|---|
S. aureus | HE681097 | 1 | 2,832,299 | 30Mb |
C. jejuni | GCA_001879185.1 | 16 | 1,629,708 | 17Mb |
E. coli | GCA_000703365.1 | 7 | 5,412,686 | 54Mb |
L. monocytogenes | GCA_001257675.1 | 39 | 2,905,183 | 31Mb |
S. enterica | GCA_000439415.1 | 2 | 4,808,805 | 50Mb |
Species | Number of Paired Files | Mean # Reads | Mean # Bases | Maximum File Size | Mean File Size |
---|---|---|---|---|---|
S. aureus | 65 | 1,608,999 | 223,069,930 | 30Mb | 30Mb |
C. jejuni | 22 | 3,361,254 | 657,706,314 | 20Mb | 18Mb |
E. coli | 9 | 2,122,840 | 356,661,903 | 55Mb | 54Mb |
L. monocytogenes | 31 | 1,777,006 | 380,854,631 | 31Mb | 31Mb |
S. enterica | 23 | 1,859,063 | 278,574,418 | 51Mb | 49Mb |
Species | # Files | Mean # kmers | Merged File Size |
---|---|---|---|
S. aureus | 65 | 2,761,345 | 77Mb |
S. aureus outbreak | 45 | 2,761,896 | 30Mb |
C. jejuni | 22 | 1,680,619 | 29Mb |
E. coli | 9 | 5,116,311 | 56Mb |
L. monocytogenes | 31 | 2,922,836 | 86Mb |
S. enterica | 23 | 4,660,457 | 53Mb |
SKA is currently only available as a preprint, so for now, if you use it, please cite: Harris SR. 2018. SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology. bioRxiv 453142 doi: https://doi.org/10.1101/453142