Benchmarks: build plasmodium

Notes

• Commit: ad47bb63a09c4b0b1f92f005e2059ce842223567
• Run time complexity: O(log n) where n is kmer size.

Results

time taken (s)	kmers	kmer size	disk memory (Gb)
1265.07	1024	5	3.5
2802.45	16384	7	5.5
6245.78	4194304	11	11
7457.18	16777216	12	14
9657.01	67108864	13	20

Commands

Example command (note: uses --all-kmers flag):

gramtools build --gram-directory /nfs/research1/zi/rff/data/pf_crosses/gram_k13 --vcf /nfs/research1/zi/projects/gramtools/standard_datasets/pfalciparum/pf3k_release3_cortex_plus_dblmsps/prg_construction/data/pf3k_and_DBPMSPS1and2.vcf --reference /nfs/research1/zi/projects/gramtools/standard_datasets/pfalciparum/pf3k_release3_cortex_plus_dblmsps/reference/Pfalciparum.genome.fasta --kmer-size 13 --all-kmers --debug

VCF:

/nfs/research1/zi/projects/gramtools/standard_datasets/pfalciparum/pf3k_release3_cortex_plus_dblmsps/prg_construction/data/pf3k_and_DBPMSPS1and2.vcf

Reference:

/nfs/research1/zi/projects/gramtools/standard_datasets/pfalciparum/pf3k_release3_cortex_plus_dblmsps/reference/Pfalciparum.genome.fasta

Output gram directories:

/nfs/research1/zi/rff/data/pf_crosses