Kspectra

Generate k-mer spectra from a complete genome to observe modalities of distribution.

Author

• Selvalakshmi (https://github.com/Selvalakshmi27)

Dependencies

• Python (3.9.12)
• matplotlib (3.5.2)
• biopython (1.79)
• pandas (1.3.4)

Usage

python kspectra.py [input.fasta] [k-mer size] [x-limit] [title]

• input.fasta = Genome sequence in fasta format
• k-mer size = Desired k-mer size (Ex: 3,9,11)
• x-limit = X-limit value for the kmer spectra graph
• title = Title for the gragh

Example

python kspectra.py e.coli_refseq.fasta 8 400 E.coli_K=8

Output

Three files are generated as the output:

• kmer_count.txt
• kmer_frequency.txt
• kmer_spectra.png

Sample output files and reference e.coli genome is found under Example folder.