Pf benchmarking

[bricoletc]

We'll put Pf PRG benchmarking figures here

Data explained:

dataset	abbreviation	description	path on yoda cluster
pf3k cortex + DBLMSP1/2	pf3k	2.4 million variant calls made using cortex on pf3k samples + Sorina's variants on msp3.4 and msp3.8 genes. Due to variant overlap this ends up as 1.56 million variant sites in the PRG as per a6e9094	/nfs/leia/research/iqbal/bletcher/projects/gramtools/datasets/pf3k_release3_cortex_plus_dblmsps/vcf/pf3k_and_DBPMSPS1and2_cleaned.vcf.gz
Same as ^^, but chromosomes 1 and 2 only	pf3k_chr1_2	88,539 sites after gramtools build	/nfs/leia/research/iqbal/bletcher/projects/gramtools/datasets/pf3k_release3_cortex_plus_dblmsps_Chroms1_2
GB4 reads mapped to Pf chroms 1 and 2	GB4_chr1_2	3.46 million Illumina WGS 100bp paired-end reads from Pf GB4 strain. The reads have been quality trimmed using trimmomatic and subsetted to Pf Chroms 1&2 (using samtools).	/nfs/leia/research/iqbal/bletcher/projects/Pf_cross_benchmark/runs/mini_Trio/samples/GB4

[bricoletc]

commit	command	dataset	kmer size	peak RAM (GBytes	average RAM (Gbytes)	run time (seconds)	CPU time (seconds)	mapped reads per CPU sec
73e4835	build	pf3k	11	38	12.4	6084	=	-
73e4835	quasimap	GB4_chr1_2 -> pf3k	11	38	37	40,315	183,405 (10 threads)	17.6
73e4835	build	pf3k_chr1_2	11	2.39	0.87	378	346	-
73e4835	quasimap	GB4_chr1_2 - > pf3k_chr1_2	11	3.37	3.31	1219	5714	566
b95321b (v1.6.0)	build	pf3k_chr1_2	11	3.45	1.80	341	328	-
b95321b (v1.6.0)	quasimap	GB4_chr1_2 - > pf3k_chr1_2	11	3.37	3.31	1041	4839	672