k-mer walking with kct. Extends a seed without needing to come back to a reference.
Installing (enter Julia package mode by pressing ] in a julia shell located in src)
(@v1.8) pkg> activate Modron
Activating project at `~/Marut/Modron`
(Modron) pkg> instantiate
Walking mode
usage: Modron.jl walk -s SEED -l LIBRARY -o OUTPUT [-r MAX_RECURSION]
[-c MIN_COUNT] [-h]
arguments:
-s, --seed SEED The seed to extend by k-mer walking.
-l, --library LIBRARY
The KCT library to use for k-mer walking.
-o, --output OUTPUT Output file. Will be in fasta format.
-r, --max_recursion MAX_RECURSION
How much the seed can be extended by k-mer
walking. (type: Int64, default: 500)
-c, --min_count MIN_COUNT
The minimum count for a k-mer to be
admissible. Should be >0. (type: Int64,
default: 1)
-h, --help show this help message and exit
Kct preparation mode
usage: Modron.jl prepare -d DATA -o OUTPUT -j JELLYFISH [-k K] [-h]
arguments:
-d, --data DATA Folder that contains ONLY jellyfish files to
turn into a Kct.
-o, --output OUTPUT The output kct file. Will be in binary format.
-j, --jellyfish JELLYFISH
Path of jellyfish executable
-k K The size of k-mers in jellyfish files (type:
Int64, default: 27)
-h, --help show this help message and exit
Known issues:
- Currently only supports building KCTs with 27mers (-k option doesn't do anything right now)
- Building from jf is slow because it relies on dumps instead of binaries
- -d argument is extremely inconveniant. Need to detect type (folder or file for single sample KCT) and only use .jf files in folder.