Struo2
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leylabmpi
Scalable creating/updating of metagenome profiling databases
Hi there, I'm continuing to troubleshoot the db-update process for a kraken2 database, and I've hit a wall at the kraken2_build step. The pipeline doesn't throw any errors; it just...
Hello! Out of curiosity, in the description of the pipeline you say that "Struo2 is designed to process one genome representative of each species, which is all that is required...
Hi, I'm near the end of the Struo2 pipeline trying to create a custom kraken2 database using gtdb r207. I've hit a wall though at the kraken2-build command, specifically one...
Hi, I want to create a Kraken2 DB with GTDB data, since it's so much more curated and reliable than NCBI. However, I do need to be able to detect...
Hi there, I am trying to update the GTDB -r207 database I have downloaded using Struo2 with my own MAGs. It is not clear how I get some of the...
Hi Nicholas, Thanks for struo2 and hosting the databases, it's a great resource. I'm using database_download.py to get the databases, but then the connection got interrupted part way through the...
Hi, I have some trouble understanding the differences in classification rates between your GTDB 207 release Kraken database and the widely used maxikraken db from 2019, which is roughly half...
Hi Nick, I am still having trouble updating my database with custom MAGs. I run snakemake using the following command and config file: [config-update.yaml.txt](https://github.com/leylabmpi/Struo2/files/10527820/config-update.yaml.txt) `snakemake --use-conda --cores 30 --configfile config-update.yaml`...
I'm using the GTDB with kraken2 and get a .txt & .report file out, but I don't understand how to convert the GTDB ID of the .txt file to NCBI...
Hi there, Thanks for developing Struo2 and for releasing the GTDB kraken2 dbs prepared with struo2. I'm using Kraken v2.1.1 and Bracken v2.8 on paired-end animal microbiome data and the...
