Other Resources for Microbial Comparative Genomics

The following tutorials and documentation will be helpful for researchers considering similar approaches.

Using the command line

A command line enables you to perform diverse operations programmatically. That is, you can do a lot of things with it, and you can automate the process for easy repetition, alteration, and sharing. You should learn how to use a command line for bioinformatics. In fact, many bioinformatics programs are run not from a user interface but from the command line. Complicating things, the Windows command line uses its own language, whereas Mac and Linux machines, which use the Unix operating system, have command lines using more common bash language.

  • For Mac and Unix operating systems, use the local command line.
  • For Windows operating systems, you can try to use git bash (latest Windows) or Ubuntu. Ideally, you establish a remote connection (SSH) to a Unix operating system, perhaps a computer cluster maintained by your organization.

Some resources for Unix:

Learning Python

If you’re a Python novice, I encourage you to take a workshop and to use Python to analyze and plot your data, so you can get practice. These guides are helpful references and will expand your toolkit.

A Whirlwind Tour of Python by Jake VanderPlas. Online Jupyter notebook with clear instruction and code examples on Python basics.

Python Data Science Handbook by Jake VanderPlas. Online Jupyter notebook with clear instruction and code examples, focused on different Python packages for data science (Jupyter Notebook, Numpy, Pandas, Matplotlib, machine learning with scikit-learn).

Metagenomics (assembly + genomics)

Going from sequencing to assembled genomes requires (1) assembly, (2) read-mapping, (3) binning genomes, and (4) bin refinement and quality check.

“A tutorial on assembly-based metagenomics” by A. Murat Eren. One example of how to perform assembly of shotgun metagenomics reads and read-mapping

A tutorial on using Anvi’o for metagenomics by A. Murat Eren. Anvi’o is the best platform for binning genomes from assembly-based metagenomics, and its creators continue to add new functions for comparative genomics.

The iRep, EukRep, dRep, and dasTool suite of programs from the Banfield laboratory. iRep is a metric for replication rate. EukRep, dRep, and dasTool aide in binning and bin refinement.

CheckM is great for assessing genome completeness and contamination.

Running things on a laptop? Sickle for read trimming, MEGAHIT for assembly, and FastTree for tree-building – these programs are relatively fast compared to their peers.

Metagenomics (amplicon sequencing)

Current best practices are to remove sequencing errors from reads, obtaining amplicon sequencing variants (ASVs) instead of operational taxonomic units (OTUs). The DADA2 tutorial worked well for me.

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