If you would like example data, please run the script 'PullData.sh' in Setup/

Additionally, if you are running this on a cluster, please remember to add your module load commands to the scripts. Alternatively, a conda environment could be used.

## Next-Generation Sequencing Upstream Analysis ##

-- Step 1: QC --

Usage:
The scripts are designed to be run in alphabetical order. For optional steps, a seperate _skip.sh script is available if the user choose not to run a certain step.

Setup: Conda environment file (environment.yml) is available in Setup/ 
To create ngs environment: conda env create -f environment.yml

Input: Raw sequence (.fastq) files in Input_data/

Workflow:
1. A_RunCheck.sh
(then enter either single_end/ or paired_end/)
2. B_RunFastqAndStats.sh
3. C_RunTrimmomaticAndSickle.sh
4. D_RunRemoveSpike.sh or D_skip.sh
5. E_RunRemoveHost.sh or E_skip.sh
6. F_RunRemoveRNA.sh or F_skip.sh
7. G_RunStats.sh
8. H_CopyResults.sh
9. I_PostQCfastq.sh (optional)

Output: cleaned sequence files (.fq) and QC stats (stats.txt, finalstats.txt) in final_QC_output/