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Lab miniproject on sourmash, first cut - GGG 298 WQ 2024 - Lab 5, Week 5

Your mission for today

Work in groups (encouraged) or individually to:

  1. Run the sourmash commands below to produce one or more comparison plots of 3 genomes. (I suggest using farm to do this, but you can do it on your own computer if you want, too.)
  2. Document and explain how to do this from start to finish in a HackMD tutorial; test the HackMD starting from scratch. (This document can start from after you log into farm.)
  3. Individually or collectively explore ways to zhuzh up the tutorial or the output.

Additional options here:

  • do the comparison with containment or ANI in addition to Jaccard;
  • write some descriptions of what you think the comparisons mean;
  • add links to the relevant parts of the documentation;
  • use the NCBI Taxonomy browser to find and download more/different genomes that you might add to the comparison, e.g. E. coli

sourmash commands

You'll need the three genome files in ~ctbrown/data/sulfo.

sourmash sketch dna a.fa.gz --name 'Sulfurihydrogenibium' -o a.sig.zip
sourmash sketch dna b.fa.gz --name 'Sulfitobacter sp. EE-36' -o b.sig.zip
sourmash sketch dna c.fa.gz --name 'Sulfitobacter sp. NAS-14.1' -o c.sig.zip

sourmash compare *.sig.zip -o sulfo.cmp

sourmash plot sulfo.cmp

This will produce a file sulfo.cmp.matrix.png.

Links

Hackmd, Markdown, and GitHub

Installing software with mamba

Additional & optional mission: try starting an RStudio Server via the Open On Demand Web interface.

This will take 2-3 hours to set up.

Note: you'll need an ssh public key of your very own in order to do this; see these two answers in the FAQ for some help.

Sign up for a farm account of your very own by going to https://hippo.ucdavis.edu/Farm/create. Use 'datalabgrp'.

Wait 2-3 hours.

Then, go to https://ondemand.farm.hpc.ucdavis.edu/ and see if you can start up an RStudio Server of your very own.