Comments (4)
shenwei356
commented on May 14, 2024
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.
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davidmaimoun
commented on May 14, 2024
So can I erase the database folder once the index created?
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shenwei356
commented on May 14, 2024
# 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 [email protected]
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davidmaimoun
commented on May 14, 2024
Thank you very much
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Related Issues (20)
- KMCP database building tutorial HOT 3
- Dealing with novel/non-sequenced species HOT 2
- long read metagenomic profiling HOT 2
- suitable for CDS and/or contig taxonomic assignment? HOT 2
- Masking prophages in bacterial genomes before building database as Phanta does HOT 2
- How to specify multiple kmer values HOT 2
- Add a tutorial of detecting specific pathogen in sequencing data HOT 1
- Detecting closest reference in custom DB HOT 4
- Report statistics of matched, unmatched reads HOT 1
- KMCP's MetaPhlAn output doesn't follow the MetaPhlAn file format HOT 3
- [Suggestion] Use score calibration when identifying proviruses and plasmids HOT 2
- ETA missing when building KMCP index HOT 4
- Merge error (number of fields < query index field) HOT 3
- Optimizing KMCP with HumGut HOT 9
- Kmcp profile empty HOT 2
- TODO: save the search result into a serializing binary file for fast downstream parsing HOT 3
- Availability of old gtdb databases? HOT 5
- coverage is greater than 100 HOT 1
- kmcp search is stucked HOT 4
- How to profile results only identify 1 species per reference HOT 6
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