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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
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