Benchmarks: Speed - simonrharris/SKA GitHub Wiki

Speed

All timings based on a 2.1 GHz AMD Opteron Processor. Other processors have been shown to produce significantly faster results.

Creating split kmer files from fasta files (ska fasta)

Species	Accession #	# Contigs	Total Length	Time Taken
S. aureus	HE681097	1	2,832,299	5.26s
C. jejuni	GCA_001879185.1	16	1,629,708	2.70s
E. coli	GCA_000703365.1	7	5,412,686	10.06s
L. monocytogenes	GCA_001257675.1	39	2,905,183	5.63s
S. enterica	GCA_000439415.1	2	4,808,805	10.88s

Creating split kmer files from fastq files (ska fastq)

Species	# Paired Files	Mean # Reads	Mean # Bases	Maximum Time Taken	Mean Time Taken
S. aureus	65	1,608,999	223,069,930	370.96	98.33s
C. jejuni	22	3,361,254	657,706,314	438.17s	271.35s
E. coli	9	2,122,840	356,661,903	266.39s	145.21s
L. monocytogenes	31	1,777,006	380,854,631	362.34s	184.29s
S. enterica	23	1,859,063	278,574,418	239.31s	118.14s

Merging split kmer files (ska merge)

Species	# Files	Mean # kmers	Time Taken
S. aureus	65	2,761,345	120.62s
S. aureus outbreak	45	2,761,896	62.53s
C. jejuni	22	1,680,619	29.96s
E. coli	9	5,116,311	41.022s
L. monocytogenes	31	2,901,968	44.34s
S. enterica	23	4,660,457	54.39s

Aligning samples from merged files (ska align)

Species	# samples	# kmers	Time Taken
S. aureus	65	7,256,936	37.31s
S. aureus outbreak	45	2,788,637	16.30s
C. jejuni	22	2,702,560	10.29s
E. coli	9	5,265,848	14.06s
L. monocytogenes	31	2,922,836	12.59s
S. enterica	23	4,966,894	19.24s

Aligning samples from merged files against a reference (ska map)

Species	Reference	Reference Size	# samples	# kmers	Time Taken
S. aureus	HE681097	2.8Mb	65	7,256,936	21.26s
S. aureus outbreak	HE681097	2.8Mb	45	2,788,637	15.50s
C. jejuni	GCA_001879185.1	1.6Mb	22	2,702,560	8.02s
E. coli	GCA_000703365.1	5.4Mb	9	5,265,848	25.25s
L. monocytogenes	GCA_001257675.1	2.9Mb	31	2,922,836	15.48s
S. enterica	GCA_000439415.1	4.8Mb	23	4,966,894	30.01s

Pairwise distances and clustering from merged files (ska distance)

Species	# samples	# kmers	Time Taken
S. aureus	65	7,256,936	38.65s
S. aureus outbreak	45	2,788,637	9.03s
C. jejuni	22	2,702,560	8.22s
E. coli	9	5,265,848	13.24s
L. monocytogenes	31	2,922,836	8.51s
S. enterica	23	4,966,894	15.71s