Week 6¶
Agenda for (02/16/2022)¶
Lecture
Phylogenetic inference
Taxonomic classification of Bacteria and Archaea
Lab exercises
Go over results from last week
binning, refinement, CheckM
Run
barrnap
to identify 16S rRNA genes in MAGsRun BLAST to identify the 16S sequences
run remote BLAST (NCBI database)
run web-based BLAST (NCBI databases + Silva)
Classify MAGs based on GTDB-TK
Construct a simple 16S rRNA-based gene tree
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