Category: BINF 6203

Read mapping and simple variants 0

Read mapping and simple variants

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...

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...

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...

NGS QC

In this exercise we will focus primarily on quality analysis and quality control of Illumina sequencing data, since that is the type of NGS data you are currently most likely to encounter in new...

Microbial community analysis with QIIME2

Microbial community analysis with QIIME2

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,...

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...