Welcome the JHU/APL Biological Sciences Datasets Directory

Reference Links

• TaxTriage
• Basestack
• Kraken2 databases to download or use
• Pre install session - metagenomics
• Kraken2
• Nextflow
• nf-core
• Docker
• Mytax2
• Pavian

Download Install Files

• Installation BAT file
• Install WSL dependencies file
• Install For Linux/Mac Script File
• Full commands unix install

Download kraken2 databases

• Test
• Standard Refseq 8 GB
• Viral (Refseq)
• Flukraken2
• All Others

Fastq Reads

• Short Reads R1
• Short Reads R2
• Long Reads Fastq

Download a Reference FASTA

• Test Metagenomics References
• Test References Index

Alignment File

• Illumina Short Reads Alignment File (BAM)
• Indexed BAM file for the above

Alignment Histogram of Coverage

• Illumina Short Reads Cov. Histogram

Kraken2 Outputs

• Miseq Kraken2 output
• ONT Kraken2 output

Krona Outputs

• ONT Omics Workshop Krona Example
• Miseq Omics Workshop Krona Example
• Long Reads Krona Output
• Short Reads Krona Output
• Long Reads Viral - Bad DB
• Short Reads Krona Viral - Bad DB