Week 6

Agenda for (02/22/2023)

• Lecture

• Phylogenetic inference

• Taxonomic classification of Bacteria and Archaea

• Lab exercises

• Go over results from last week

  • binning, refinement, CheckM

• Install the following tools on Cerberus:

  • barrnap

  • seqtk

  • mafft

  • trimal

  • IQ-Tree (iqtree)

• Run barrnap to identify 16S rRNA genes in MAGs

• Run BLAST to identify the 16S sequences

  • run remote BLAST (NCBI database)

  • run web-based BLAST (NCBI databases + Silva)

• Construct a simple 16S rRNA-based gene tree

• Install GTDB-Tk

• Classify MAGs based on GTDB-Tk

Relevant papers to read

Phylogenetic inference

• Kapli et al (2020) Nature Reviews Genetics (https://www.nature.com/articles/s41576-020-0233-0)

Taxonomic classification

• Parks et al (2018) Nature Biotechnology (https://www.nature.com/articles/nbt.4229)

Other useful resources

Webinar on using NCBI 16S sequences for phylogenetic analyses

https://www.youtube.com/watch?v=wBbh_1vXgsY