sauloal / MinEncCanKmer

Minimal encoding of canonical k-mers (Source: https://gitlab.ub.uni-bielefeld.de/gi/MinEncCanKmer)

MinEncCanKmer

Minimal encoding of canonical k-mers

Source: https://gitlab.ub.uni-bielefeld.de/gi/MinEncCanKmer

Compilation

gcc -O3 -D_FILE_OFFSET_BITS=64 -I./ -pthread -mbmi -o canonical fasta.c canonical.c -lm

Usage

./canonical <fasta> <k> <b>

where

• fasta is a (multiple) fasta file
• k is the k-mer length, optional, default 5, maximum 31
• b is the number of buckets, optional, default 4

Output: distribution of k-mers to buckets

2-bit encoding

To switch to standard 2-bit encoding, (uncomment) the following lines:

// process_string(seq,k,threads,t)
   process_string_std(seq,k,threads,t)

General alphabets

For encoding canonical k-mers on general (non-DNA) alphabets, Python scripts are provided in the according subfolder, where minenc.py outputs the encoding of all k-mers for a given alphabet size, and minenc_rc.py encodes considering reverse complementation.

License

• fasta.c and fasta.h are borrowed from FragGeneScan-Plus.
• MinEncCanKmer is licensed under the GNU general public license.