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Clearly, there are many file formats that we can use this script to convert.  In our case, we are moving from genbank to fasta, so the commands we would execute to produce and view the FASTA files would look like this:

cd $WORK/core_ngs/references
bp_seqconvert.pl --from genbank --to fasta < vibCho.O395.gbk > vibCho.O395.fa
mv vibCho.O395.fa fasta/
grep ">" fasta/vibCho.O395.fa
less fasta/vibCho.O395.fa

Now we have a reference sequence file that we can use with the bowtie2 reference builder, and ultimately align sequence data against.

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bowtie2 -x vibCho/vibCho.O395.fa -U fastq/cholera_rnaseq.fastq.gz -S cholera_rnaseq.sam

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