Merged pull requests:
- update readme #8 (ssjunnebo)
- fix bowtie regex #7 (andrewjpage)
- pass output directory through in download #6 (andrewjpage)
- annotate bacteria #5 (andrewjpage)
- dont duplicate strain name #4 (andrewjpage)
- Parallelise download, fix samtools versions #3 (andrewjpage)
- working #2 (andrewjpage)
- script to prepare reference files #1 (andrewjpage)