Tutorials for Genomics
In previous iterations of this course, we’ve used the RAST/SEED servers to perform annotation. RAST is a highly regarded genome annotation pipeline, and you will easily be able to justify using it to reviewers...
For today’s class, I have prepared a shared dropbox folder that contains the following items: sequence reads from one of the better chloroplast genome samples generated with our Ion Torrent instrument ERR008613 (a set...
One of the main sequence analysis tasks we want to perform on the UEGP dataset is the evaluation of antibiotic resistance potential in the wastewater microbial community. We have examples of analytical approaches to this...
This summer, my students and I are working through analysis of wastewater microbiome sequencing data. The analysis includes 3 timepoints, 11 sampling points, 2 wastewater treatment streams, and 3 replicates of each sample. 198 samples...
We’re not quite ready to launch into full-on python scripting just yet — so here’s a little add-on to your final bash project, to help make use of the output files you generate. Why...
Today’s lab task is preparation for developing a script that will assemble a batch of small genome sequence data sets. In our script development process there are four main steps: Figure out the pipeline...
To get around the problems with the software installs in the lab (and that some of you are having installing corset on your own) here is another way to get a full DE gene...
In this case study, I attempted to improve on the draft assembly of a bacterial genome by combining the original and new data, and using new bioinformatics tools that have become available since we first assembled the genome and...
I just happen to have a file with 960,628 lines of personal SNP data from 23 and Me burning a hole in my hard drive. I’m one of the lucky people who gets 23...
I’m running my own Galaxy and I want to use it to run the SPAdes assembler as part of a Galaxy pipeline, instead of running SPAdes at my command line with shell scripts. Ostensibly, this...