---
# System prepended metadata

title: Bash Workflow

---

# Bash Workflow

#Convert to fastq - I haven't used these but stack overflow recommends
	#option 1) phred (http://www.phrap.org/consed/consed.html#howToGet)
	#option 2) TraceTuner (https://sourceforge.net/projects/tracetuner/)
#trim based on quality
	#http://www.usadellab.org/cms/?page=trimmomatic
#align sequences
	#https://www.drive5.com/muscle/ 
#cut off primers
	#https://cutadapt.readthedocs.io/en/stable/
#blast sequences - entire workflow here, pick and choose as needed: https://angus.readthedocs.io/en/latest/running-command-line-blast.html
	#create blast database
	#blast sequences to database
    
    
# If you want to play with python a little, you could turn this into a snakemake workflow (which is super cool and much better for running pipelines, but has a bit of learning curve). This will work fine though. If you run into issues I'm happy to help!
## snakemake example: https://snakemake.readthedocs.io/en/stable/tutorial/basics.html


# Same workflow in Bash and Snakemake 
## Bash: https://angus.readthedocs.io/en/2019/bash_automation.html
## Snakemake: https://angus.readthedocs.io/en/2019/snakemake_for_automation.html