Sequence Assembly
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...
Genome Intelligence Blog
Sequence Read QC
DNA Sequencing is a continually evolving technology, with new platforms becoming available each year, all designed with the aim of reducing the cost and increasing the speed of large sequencing projects. As you can...
Prepare Your Computer
Many of the assignments in BINF 6203 are scaled so that you can complete them on a reasonably powerful laptop without using the University Research Computing cluster. That said, in order to do the...
BINF 6203: 16S rRNA classification with QIIME
This tutorial makes use of the data from the NC Urban Microbiome Project, a collaboration seeded by the Department of Bioinformatics and Genomics and involving participants from our department as well as Civil Engineering,...
BINF 6203: Read Mapping
Mapping short sequence reads to a reference sequence is a common task in genomics. Many different results can be extracted from a mapped sequence, depending on the original experimental design that produced the sequence...
BINF 6203: Bacterial genome annotation with prokka
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...
BINF 2111: Genome Horoscope (eye color — part 2)
Your mission for today is to write a script that checks a 23 and Me genotype file for several groups of SNPs that are associated with blue eyes. The SNPs in question are in...
BINF 2111: Genome Horoscope — eye color (Part 1)
In this week’s exercise, we’re going to practice loops and lists in Python by looping through a 23 and me file to pull out data that matches a list of SNPs of interest. Before...
UEGP: Detecting antibiotic resistance determinants
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...
Summer Research: Urban Environmental Genomics Project
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...