Installation KrakenUniq🐙
Make sure you have the latest version of KrakenHLL installed.
git clone https://github.com/fbreitwieser/krakenuniq.git
cd krakenuniq
bash install_krakenuniq.sh $HOME/bin/
export PATH=$PATH:$HOME/bin/
DBNAME=bacteria
krakenuniq-download --db $DBNAME taxonomy
krakenuniq-download refseq/bacteria --db $DBNAME --dust --threads 20
krakenuniq-build -build --db $DBNAME --jellyfish-hash-size 6400M \
--taxids-for-sequences --taxids-for-genomes --threads 8
dump_taxdb taxDB taxonomy/names.dmp taxonomy/nodes.dmp
DBNAME=virus-neighbors
krakenuniq-download --db $DBNAME taxonomy
krakenuniq-download refseq/viral/Any --db $DBNAME --dust --threads 8
krakenuniq-download viral-neighbors --db $DBNAME --dust --threads 8
krakenuniq-build -build --db $DBNAME --kmer-len 25 \
--jellyfish-hash-size 6400M \
--taxids-for-sequences --taxids-for-genomes --threads 8
dump_taxdb taxDB taxonomy/names.dmp taxonomy/nodes.dmp
With you sunbeam conda environemnt activated,
- Clone into your Sunbeam directory:
git clone https://github.com/zhaoc1/sbx_krakenhll
- Add the new config options to your config file
cat sunbeam/extensions/sbx_krakenhll/config.yml >> sunbeam_config.yml
- Run time
snakemake --configfile my_config.yml all_krakenhll
- Fun part
Try to play with krakenhll-extract-reads
to get the classified reads for your favoriate taxid 😬