Create an index without create the database

[davidmaimoun]

Hello Dr Shen,

Can I create an index without create the database ? Because the folder takes memory.

If my interest is to indexing sequences and run some query, is it possible to use the tool without the db creation step ?

Best,

[shenwei356]

I'm afraid you have to create the database with kmcp compute and kmcp index before searching.

And Most tools need an index step for search.

[davidmaimoun]

So can I erase the database folder once the index created?

[shenwei356]

# compute k-mers
kmcp compute -k 21 --split-number 10 --split-overlap 100 \
    --in-dir genomes/ --out-dir genomes-k21-n10

# index k-mers
kmcp index --false-positive-rate 0.1 --num-hash 1 \
    --in-dir genomes-k21-n10/ --out-dir genomes.kmcp

# ------------------------------------------------------------------------------
# Here, the genomes-k21-n10/ folder created by 'kmcp compute' could be deleted.
# ------------------------------------------------------------------------------
# delete temporary files
# rm -rf genomes-k21-n10/

# search    
kmcp search --db-dir genomes.kmcp/ test.fa.gz --out-file search.kmcp@db1.kmcp.tsv.gz

[davidmaimoun]

Thank you very much