Benchmarks: File Sizes - simonrharris/SKA GitHub Wiki

File sizes

Creating split kmer files from fasta references (ska fasta)

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

Creating split kmer files from fastq files (ska fastq)

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

Merging split kmer files (ska merge)

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