We have pre-built Kraken2 (v2.1.2) and Bracken (v2.9) reference database packages based on the PBac v2 database, which can be downloaded from this website. If analysis of giant panda gut microbial metagenomic data is required (e.g., calculating relative abundance, taxonomic annotation of contigs/reads), the pipeline below can be used for analysis.

Fristly, please download the precomputed Kraken2 (version 2.1.2) and Bracken (version 2.9) reference databases built from the PBac v2 database via our website. ​ Choose the download source (figshare or our local website) based on your internet connection speed and reliability.

Then, uncompress the pre-built Kraken2 reference database :

tar -zxvf kraken2_Pbac_v2_Com50_Con10.tar.gz

You can performed giant panda gut microbial metagenomic data with the following commands:

kraken2 --db ~/kraken2_Pbac_v2_Com50_Con10 --use-names --threads 48 --report-zero-counts --classified-out kraken2/${id}_classified#.fq --report-zero-counts --report kraken2/${id}_kraken2.report --output kraken2/${id}_kraken2.out ${id}_paired_1.fastq ${id}_paired_2.fastq
bracken -d /public1/home/scb4940/softwares/kraken2_2024 -i kraken2/${id}*.report -o bracken/${id}.S.bracken -w bracken/${id}.S.bracken.report -r 150 -l S -t 8  # species level