Projects created in my bioinformatics class.

• zeus: Command line program, written in python, that runs other programs to assemble and annotate a bacterial genome.
• multihmmer_script: Simple bash script that takes query sequences in a single fasta file and a directory with fasta files that each contain proteins from a given organism. With the query a MSA is generated with muscle. Afterwards, a HMM is generated with hmmbuild.Using hmmsearch the HMM created from hmmbuild is used to search in the fasta files that are in the given directory for similar proteins to the query sequences.
• auto_annotate: Bash script to annotate prokayotic genomes using prokka. Just give the script a directory with genomes in it and prokka will be used to annotate them.