Hi, I would like to build a custom kraken database using specific NCBI sequences for e.g., plants. I tried the RefSeq plant database, however it seems to consist primarily of agricultural species, and not species I'd expect to find in my...
but rather simply provide the name of the directory in which they are stored. Kraken 2 allows both the use of a standard database as well as custom databases; these are described in the sections [Standard Kraken 2 Database] and [Custom Databases] below, respectively. ...
kraken-build --download-library bacteria --db $DBNAME kraken-build --add-to-library chr1.fa --db $DBNAME Step1:Create k-mer set: Jellyfish -> database.jdb 步骤2就是利用Jellyfish软件切割k-mer,生成database.jdb文件, 文件内容是 “k-mer: count”。 Jellyfish是CBCB(Center for Bioinformatics...
This seems to be doing the job. If I need a custom database, I'll try modifying the rsync_from_ncbi.pl file. 👍 1 ctuni reacted with thumbs up emoji jenniferlu717 added the download issue kraken2-build --download-library issue label Mar 14, 2022 Sign up for free to join this ...
data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.py "value": custom_database_name, "name": custom_database_name, "path": custom_database_name "value": database_value, Member bgruening Oct 18, 2024 The value is the path, correct? Why? Co...
database are here: gs://gbsc-gcp-lab-bhatt_user-bsiranos/kraken_db_construction_dec2021/add_genomes # add the custom genomes that go into refseq # refseq has mouse and crassphages # mouse is easy kraken2-build --add-to-library add_genomes/mm10.fa --db refseq --threads 8 # ...
First, using Metaphlan to construct the database would likely void some of the advantages of Kraken2 over Metaphlan in terms of recall. Second, having to build the database rather than have it inputted pre-made would increase computational expense. Some questions: If we added a section on ...
# Create a custom taxonomy database flextaxd --taxonomy_file taxonomy.tsv --database .ftd # Export database to NCBI format flextaxd --dump # Print database statistics flextaxd --stats # Get help flextaxd --help Requirements Python >=3.6 Additional dependencies vary based on executed func...
To build a protein database, the--proteinoption should be given tokraken2-build(either along with--standard, or with all steps if building a custom database). Custom Databases We realize the standard database may not suit everyone's needs. Kraken 2 also allows creation of customized database...
To build a protein database, the--proteinoption should be given tokraken2-build(either along with--standard, or with all steps if building a custom database). Custom Databases We realize the standard database may not suit everyone's needs. Kraken 2 also allows creation of customized database...