Welcome to the Fungal Genomics and Bioinformatics Workshop!

Here we will post information needed for the workshop: - software packages we use - how to use the packages

We will use a lot of Linux command line, for reminders have a look at the Help page for technical stuff.

References to the papers about the software and other helpful papers you can find in the References chapter.

Note

This project is under active development.

Contents

• 0.1. Brief introduction to polyphasic taxonomy
• 0.2 Basecalling of ONT reads
• 1. Data Quality Check (QC)
  • Illumina QC
  • Oxford Nanopore QC
• 2. Data Trimming
  • Illumina data trimming
  • Oxford Nanopore data trimming
• 3. Genome assembly
  • Illumina only datasets
  • Oxford Nanopore only datasets
  • Hybrid assembly
• 4. Genome Assembly QC
  • Assembly statistics
  • Completeness check (before polishing)
  • Contamination and overall statistics check
    • Create meta data yaml file
    • Create a BlobDir
    • Use BLAST and UNIPROT to identify contaminations
      • BLAST
      • UNIPROT
      • Adding BLAST and UNIPROT results to BlobDir
    • Adding mapping coverage
      • Using minimap2 to map reads
      • Adding mapping coverage of short and/or long reads to BlobDir
    • Add BUSCO scores
      • Run BUSCO if necessary
      • Add to BUSCO results to BlobDir
    • Add links to BlobDir
    • Open dataset in BlobToolKit Viewer
  • ITS extraction to identify with BLAST
• 5. Polishing the assembly
  • Polishing Illumina and/or hybrid data
  • Polishing Oxford Nanopore data
    • Polishing four rounds with Racon
    • Polishing with Medaka
    • Polishing with Homopolish
• 5.1 Dealing with heterozygous genomes
  • Using purge_dupsto create a haploid genome assembly
• 6. Genome annotation
  • Masking repeats
  • Gene prediction
  • Gene identification
• 7. Comparative genomics
• 8. Phylogenomics
• Help page for technical stuff
  • Install and usage of PuTTy (Windows)
  • Linux basic command usage
• References