MASH vs OMH

Singularity container

Build singularity container:

singularity build container.img container.def

GOS FTP

# Get root file listing
wget --no-remove-listing ftp://ftp.imicrobe.us/projects/26/

# Get Assembly file
wget ftp://ftp.imicrobe.us:21/projects/26/CAM_PROJ_GOS.asm.fa.gz

# Download all sample reads
wget -r --no-parent -A *.fa.gz ftp://ftp.imicrobe.us/projects/26/samples

Some notes:

• OMH better on long reads, depends on the missmatchs of the data
• Select 2 biggest samples of each data source
• Estimate runtime
• Get the directories where the data is already downloaded
• OMH params -k 10 -l 1,2,3 -m 10
• Do average of minimum distances

Steps:

• Download 3 datasets (2 similar and 1 distant) and sample ~1000 reads

• Make sketches

• Compute distance matrix

• Make histogram

• Run hypothesis testing?

• Running OMH distance 8 min 20 sec for 3 pair sets