Metagenomics-Index-Correction
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rrwick
Torsten Seemann (@tseemann) suggested I share this script I wrote a while back: ``` #!/bin/bash # Download pre-made Kraken2 database based on GTDB r89 # https://github.com/rrwick/Metagenomics-Index-Correction # https://monash.figshare.com/articles/GTDB_r89_54k/8956970 # https://www.biorxiv.org/content/10.1101/712166v1...
For your extension of the GTDB, it would be great if you could provide the full Kraken folder from which to build a Braken database. i.e. from Braken's documentation >...
Hello everyone, I building GTDB databases to be used along with Kraken2. I was wondering if it was possible to add viral refseq sequences while building kraken2 databases? GTDB consists...
I'm trying to replicate what you did to create a kraken2 index using GTDB r95 using your script however you don't list the `kraken2-build` command you used. I tried using...
Hi, I was wondering if you also tried dereplication threshold other than 0.005 (i.e. something between 0.005 and the original 0.05 from GTDB)? I am trying to find the best...
tax_from_gtdb.py did not prepare all the genome sequence .fna files avaialable in the genome/ folder. I downloaded and extracted the latest GTDB reference database (24706 genome .fna files) into a...
$ tar -tf gtdb_r89_54k_kraken2_full.tar $ hash.k2d $ tar: Skipping to next header $ tar: Exiting with failure status due to previous errors I tried the download twice with the same...
It would be great to have a precompiled MetaMaps database for long read classification. Cheers.
Hello Ryan I am interested in using your kraken2 databases. I am curious to know why there are diffeerent size files? How do they differ? Cheers, Andy
