- Place your paired fastq files in numbered folder (e.g. folder_1, folder_2, folder_3) for better parallization.
- Make sure to put your own account name in the batch script!
- Submit .slurm scripts to scheduler and just run .sh scripts on head node.
| Script Title | Use |
|---|---|
| 0_run_bbmap.slurm | bbduk.sh and dedupe.sh |
| 1_run_kraken.slurm | Decontamination |
| 2_run_jellyfish.slurm | Histogram Generation |
| 3_run_compile_hist_data.sh | Compiling Necessary Data for RESPECT (do not submit to slurm scheduler) |
| 4_run_respect_full.slurm | Runs RESPECT |
| 5_run_downsample.slurm | Uses seqtk to downsample data |
| 6_run_jellyfish_downsampled.slurm | Histogram Generation on Downsampled Replicates |
| 7_run_compile_downsampled_data.sh | Compiles Necessary Data Again (do not submit to slurm scheduler) |
| 8_run_respect_downsampled.slurm | Runs Final RESPECT Run |
Notes:
- You may have to change the SCRIPT_DIR variable from 0_run_bbmap.slurm to the path where the scripts have been placed.
- Install kraken2 (export to PATH if installed via github)
- Download PFP-Plus 16 and add to directory where analyses are being run.