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    "## Week 6"
   ]
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   "metadata": {},
   "source": [
    "### Agenda for (02/16/2022)"
   ]
  },
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   "source": [
    "- Lecture\n",
    "  - Phylogenetic inference\n",
    "  - Taxonomic classification of *Bacteria* and *Archaea*\n",
    "- Lab exercises\n",
    "  - Go over results from last week\n",
    "    - binning, refinement, CheckM \n",
    "  - Run `barrnap` to identify 16S rRNA genes in MAGs\n",
    "  - Run BLAST to identify the 16S sequences\n",
    "    - run remote BLAST (NCBI database)\n",
    "    - run web-based BLAST (NCBI databases + Silva)\n",
    "  - Classify MAGs based on GTDB-TK\n",
    "  - Construct a simple 16S rRNA-based gene tree"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Relevant papers to read"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Phylogenetic inference**\n",
    "\n",
    "- Kapli et al (2020) Nature Reviews Genetics (https://www.nature.com/articles/s41576-020-0233-0)\n",
    "\n",
    "**Taxonomic classification**\n",
    "\n",
    "- Parks et al (2018) Nature Biotechnology (https://www.nature.com/articles/nbt.4229)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Other useful resources"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Webinar on using NCBI 16S sequences for phylogenetic analyses**\n",
    "- https://www.youtube.com/watch?v=wBbh_1vXgsY"
   ]
  }
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