Category: BINF 6203

Read mapping and variant calling

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...

Pangenome analysis with PanX

PanX is a program for pangenome analysis and production of core genome phylogenies. The PanX analysis tools are available as a github package for custom genome analyses, and also as a web server. The...

Genome Comparison with Mauve

There are many ways to compare genomes, and these comparisons provide different kinds of information about evolutionary history and shared function. First, how do you decide which genes are “the same” across multiple genomes,...

Genome annotation with prokka

Why use Prokka? First, because in a benchmark test it has been shown to be as or more accurate at reproducing known annotation than RAST or xBASE2 in most annotation categories. Second, because it’s...

Access and use genome track data

Genome browsers are designed to get different types of genome track data together using the common reference system of genomic coordinates. Often you’re more interested in manipulating whole sets of data, rather than just...

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...

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

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...