cgr-png

Lossless compression of kmer counts with chaos game representation. Here are the steps for generating 12mer image for human genome.

Download data

wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/GRCh38.primary_assembly.genome.fa.gz
gunzip GRCh38.primary_assembly.genome.fa.gz

Prepare kmer count data

We used KMC for kmer counting. You can install KMC in Debian/Ubuntu distros by sudo apt install kmc

kmc -b -fm -k12 -ci0 -cs5000000 GRCh38.primary_assembly.genome.fa  hg38_kmc_12mer_counts .
kmc_dump hg38_kmc_12mer_counts hg38_kmc_12mer_counts.tsv

Convert kmer counts to PNG image

We provided Python script (might be slow) to convert kmer counts to image

cat hg38_kmc_12mer_counts.tsv | python counts2image.py 12 > hg38_12mer.png

For faster processing we also provided equivalent Golang version. Please compile the script and make it executable before using it.

# run following two lines only once
go build counts2image_fast.go
chmod 755 counts2image_fast.go

cat hg38_kmc_12mer_counts.tsv | ./counts2image_fast 12 >| go-hg38_12mer.png

Extract kmer counts from PNG images

python image2counts.py hg38_12mer.png > 12mer-hg38.tsv

# go version, build and make executable for once
go build image2counts_fast.go
chmod 755 image2counts_fast

./image2counts_fast hg38_12mer.png > 12mer-hg38-go.tsv