NBIS-Metagenomics
env
Setup
Installation
Quick start guide
Using the examples
Using your own data
General configuration settings
The sample list file
How to run on UppMax/Hebbe (SNIC resources)
Preprocessing
Preprocessing reads
Trimmomatic
Cutadapt
Phix filtering
Fastuniq
SortMeRNA
Markduplicates
Read-based classification
Classify reads
Centrifuge
Kraken2
Filtering results
Centrifuge filtering
Sourmash filtering
Bowtie2 alignments
Output
De-novo assembly
Assembly
Reports
Annotation of coding sequences
Protein family annotation
Taxonomic annotation
Generating required database files
Binning metagenomic contigs
Settings
Binning tutorial
Splitting up the example
NBIS-Metagenomics
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