Comments (5)
shenwei356
commented on May 14, 2024
1
Yes, they are still there, follow the download page: https://1drv.ms/u/s!Ag89cZ8NYcqtjHwpe0ND3SUEhyrp?e=QDRbEC
path: kmcp/v2021.12/metagenomic-profiling
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shenwei356
commented on May 14, 2024
1
Oh .... I see. Sorry, I don't think I have a prebuilt database for gtdb r207. But you can make one, it's easy.
Please follow these steps: https://bioinf.shenwei.me/kmcp/database/#gtdb . Please skip the step of "Masking prophage regions and removing plasmid sequences with genomad (optional)".
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fplazaonate
commented on May 14, 2024
1
# reference genomes are split into 10 chunks with 100bp overlap
I think it is 150bp
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fplazaonate
commented on May 14, 2024
1
I successfully created the database.
Thanks.
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fplazaonate
commented on May 14, 2024
Hi @shenwei356 ,
I have just reopened the issue.
The gtdb v2021.12 database has 47,894 representative genomes.
It corresponds to gtdb r202 not gtdb r207 (https://gtdb.ecogenomic.org/stats/r202).
Do you have a prebuilt database for gtdb r207?
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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
- 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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