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SilasK / Krak

Snakemake for flexitaxd and Kraken2
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Build? What do you mean? #2

Open luozhy88 opened 2 years ago

luozhy88 commented 2 years ago

HI，in the config, is this a result about the green_genes_taxonomy.tsv ? How can I create a green_genes_taxonomy.tsv. On the other hand, Do you need a directory or a file about genome_folder?

Build

build_db_name : "kraken_db" taxonomy: "green_genes_taxonomy.tsv" genome_folder: /data2/zhiyu/database/sunbeam/host_hsa #/home/kiesers/s/HumanUnifiedCatalog/gff/fasta

SilasK commented 2 years ago

The build section is only necessary if you want to create a new Kraken2 database. In this case you would need to have a bunch of genome fasta files in the genome_folder and their taxonomy. I found it the simplest to use the green genes taxonomy format but it is possible to use other format.

But I think it's not what you are trying to do.

Also, this pipeline starts with quality-controlled reads.