Category: genomics

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...

UEGP: Detecting antibiotic resistance determinants

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

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...

BINF 2111: Exploring SNPs with bedtools (Lab)

BINF 2111: Exploring SNPs with bedtools (Lab)

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...

BINF 2111: Assembly at the Command Line (Lab)

BINF 2111: Assembly at the Command Line (Lab)

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...

Sidebar: DE with Tuxedo pipeline #usegalaxy

Sidebar: DE with Tuxedo pipeline #usegalaxy

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...

Under the hood: V. vulnificus JY1305

Under the hood: V. vulnificus JY1305

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...