13. Downloads

13.1. Tools

• Miniconda installer [ EXTERNAL ]

• Minikraken database [ EXTERNAL ]

• Centrifuge database [ EXTERNAL ]

• Krona taxonomy database [ DROPBOX ]

13.2. Data

• Quality control: Raw data-set [ DROPBOX ] [ OSF ]

• Quality control: Trimmed data-set [ DROPBOX ] [ OSF ]

• Genome assembly: Assembled data-set [ DROPBOX ] [ OSF ]

• Read mapping: Mapping index (bwa) [ DROPBOX ] [ OSF ]

• Read mapping: Mapped data [ DROPBOX ] [ OSF ]

• Variant calling: Called/filtered variants [ DROPBOX ] [ OSF ]

• Genome annotation: GFF annotation file [ DROPBOX ] [ OSF ]

• Variants-of-interest: SnpEff annotated vcf-file [ DROPBOX ] [ OSF ]

13.3. Tutorial

• A PDF version of this tutorial is available here.