Building and querying a kraken2 database

Explore building and querying a kraken2 database by downloading genomes for 12 bacteria, building the database, and mapping sequencing reads to compare healthy and SIBO samples.

Build and query a kraken2 database by collecting bacterial genomes, selecting sequences, and automating their addition with a script that updates the library and mapping files while masking low-complexity regions.

Learn about kraken2 database variants beyond the standard database, including downloadable libraries for bacteria, viruses, protozoa, and human sequences, and how to build or augment the database with specific libraries.

Build a kraken2 database by downloading taxonomy into the database, inspect accession to taxid mappings, and run the build with the kimberlin flag 41 to create and verify the database.

Inspect your kraken2 database to verify its structure and contents using the inspect command, exploring the hierarchical taxonomic levels, taxon IDs, and numbers at each node.

Explain taxonomy basics and the eight main levels: domain, kingdom, phylum, class, order, family, genus, species. Illustrate the three domains and issues like gram staining with pathogenic E. coli.

Download two Illumina data sets for small intestinal bacterial overgrowth from the SRA database, producing fastq files with fasterq-dump, then prepare to run them against the SIBO database.

Run a kraken2 query against the database, with paired or single reads. Specify output and report files, then interpret the taxonomic output and unclassified reads.

interpret a kraken2 report by decoding its six columns, including the percent of reads mapped at each taxonomic level, then examine family-level mappings and sample-to-sample correlations.

Explore querying a Kraken2 database with a Parkinson's gut sample from a SIBO dataset to identify bacteria linked to Parkinson's, including a 42.1% mapping to a Parkinson's-associated bacterial family.

Visualize metagenomic results with Pavian, an online tool that uploads partitioned kraken2 outputs and displays taxonomic breakdowns, Sankey diagrams, and ranked tables of classified reads.

Learn how kraken2 environmental variables govern thread counts and database paths, override defaults with a flag, and configure PATH to access the database across directories.

Produce MPA style reports from Kraken2 outputs, detailing taxonomic classifications and reads mapped to each category, and generate heat maps showing intensity by sample and species.

Build and query a Kraken2 database by adding custom or standard virus and organism genomes, then classify unknown metagenomic samples and visualize results with MEGAN6.