ref

build reference database

mkidr ref/

kraken2:SILVA 16s

https://ftp.arb-silva.de current version:138_2

mkdir -p ref/kraken2/16S_SILVA138_2
docker run -v /staging/fanyucai/eDNA/ref/kraken2/16S_SILVA138_2:/ref/ edna sh -c 'export PATH=/opt/conda/bin:$PATH && sed -i s:138_1:138_2: /opt/conda/share/kraken2-2.1.3-4/libexec/16S_silva_installation.sh && kraken2-build --special silva --db /ref/ --threads 16 --kmer-len 51'

qiime:Greengenes2

https://ftp.microbio.me/greengenes_release/current/

<version>.backbone.v4.nb.qza

<version>.backbone.full-length.nb.qza

Naive Bayes classifier trained on the V4 region, and separately, the full length 16S
from the backbone sequences. NOTE: mitochondria and chloroplast sequences
are included.

dada2:SILVA

https://benjjneb.github.io/dada2/training.html

docker run -v :/raw_data -v :/ref/ edna sh -c 'export PATH=/opt/conda/bin/:$PATH && /opt/conda/bin/blastn -query /raw_data/ -subject /ref/ -task megablast '