Performance

HapFlow has been designed for (and tested on) mixed-bacterial strains. The time to create the flow file scales linearly with coverage and variant number. There is also an option to only examine a subsection of the variants in a VCF file; this should allow HapFlow to be used to visualise subsections of much larger genomes.

On a moderately powered laptop it can generate a flow file for small bacteria (Such as C. pecorum) with moderate coverage (~200x) in around 10 minutes using <1GB of memory. Visualising this data also uses <1GB of memory.

In comparison, HapFlow takes ~4 hours to generate a flow file for Psueodomonas aeruginosa (genome size 6 MBp) with 300x coverage and over 200 thousand called variants. Generating the flow file uses <1GB of memory, visualising the flow files uses <3GB of memory.