Category: genomics

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...

BINF 6215: command line variant calling

BINF 6215: command line variant calling

Define the problem Ion Torrent sequence for 12 tomato varietal chloroplasts One reference genome (NC_007898) Map the reads to the reference Identify variants specific to each strain Identify the tools Obviously you’ve done some...

Galaxy NGS 101: Synechocystis remix

Galaxy NGS 101: Synechocystis remix

I made a previous version of this tutorial with some actual expression data from our lab. This version uses an already-normalized set of single-end transcriptome data from Synechocystis PCC 6803. (Normalized data here). Trimming and...

BINF 6215: Using bpipe

BINF 6215: Using bpipe

bpipe is part of a relatively recent trend to build pipeline manager tools that work at the command line. Other examples of this trend are Snakemake, Leaf and nestly.  You may want to consider using...