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@ -4,9 +4,15 @@
# Cow/calf Rumen Metagenomics Pipeline
An end-to-end script to convert Illumina shotgun sequences and metadata into full-blown diversity tables and visualizations. Of course, it's focused on the rumen and dam/calf relationships, but is widely applicable to other systems.
An end-to-end script to convert Illumina shotgun sequences and metadata into
full-blown diversity tables and visualizations. Of course, it's focused on the
rumen and dam/calf relationships, but is widely applicable to other systems.
Written entirely during Spring Semester 2019 for work done in [Dr. Hannah Cunningham-Hollinger's lab][hollinger-lab] at the University of Wyoming, computed on UW's [ARCC High-performance servers][arcc-servers] and presented as a [poster] at the Western Section American Association of Animal Science annual meeting.
Written entirely during Spring Semester 2019 for work done in [Dr. Hannah
Cunningham-Hollinger's lab][hollinger-lab] at the University of Wyoming,
computed on UW's [ARCC High-performance servers][arcc-servers] and presented as
a [poster] at the Western Section American Association of Animal Science annual
meeting.
## Prerequisites
@ -17,7 +23,8 @@ You will need access to the following commands/programs:
- `source activate` ([Miniconda])
- `qiime`, `biom` (Install within [conda environment] named `qiime2`)
If working on a HPC, contact your department to find out how to get access to these commands.
If working on a HPC, contact your department to find out how to get access to
these commands.
## Usage
@ -27,7 +34,12 @@ Clone the script files
git clone https://github.com/MillironX/cowcalf-rumen-metagenomic-pipeline.git
```
Create a directory with all forward- and reverse- read files in it, named as `<SAMPLEID>_R1_001.fastq.gz` for forward-reads and `<SAMPLEID>_R2_001.fastq.gz` for reverse-reads. Add a [QIIME2-compatable metadata file][qiime2-metadata] named `metadata.tsv`, text files containing the minimum and maximum rarefaction values names `rarefaction.min.txt` and `rarefaction.max.txt` and copy all of the code files into it. It should look like
Create a directory with all forward- and reverse- read files in it, named as
`<SAMPLEID>_R1_001.fastq.gz` for forward-reads and `<SAMPLEID>_R2_001.fastq.gz`
for reverse-reads. Add a [QIIME2-compatible metadata file][qiime2-metadata]
named `metadata.tsv`, text files containing the minimum and maximum rarefaction
values names `rarefaction.min.txt` and `rarefaction.max.txt` and copy all of the
code files into it. It should look like
```plaintext
.
@ -51,7 +63,11 @@ Create a directory with all forward- and reverse- read files in it, named as `<S
### With Slurm
These scripts are preconfigured for use with [Slurm] and [Lmod]. Everything is very basic, and should work on any Slurm configuration. Before use, be sure to replace the provided credentials with your own in `main.sh`, `fastq-to-taxonomy.sh`, `sample-classifier.sh`, and `sample-regression.sh`, then run
These scripts are preconfigured for use with [Slurm] and [Lmod]. Everything is
very basic, and should work on any Slurm configuration. Before use, be sure to
replace the provided credentials with your own in `main.sh`,
`fastq-to-taxonomy.sh`, `sample-classifier.sh`, and `sample-regression.sh`, then
run
```bash
sbatch main.sh
@ -59,7 +75,9 @@ sbatch main.sh
### Without Slurm
Edit `main.sh` and remove every call to `srun` (including its cli options), replace every instance of `$SLURM_NTASKS` with the number of parallel threads you wish to run, and comment out every line that starts `module load`. Then run
Edit `main.sh` and remove every call to `srun` (including its cli options),
replace every instance of `$SLURM_NTASKS` with the number of parallel threads
you wish to run, and comment out every line that starts `module load`. Then run
```bash
./main.sh
@ -67,11 +85,14 @@ Edit `main.sh` and remove every call to `srun` (including its cli options), repl
## Future Work
This project is finished. It is meant to be a reference and an inspiration, but nothing more. I do not intend to update the code now (as embaressing as it might be).
This project is finished. It is meant to be a reference and an inspiration, but
nothing more. I do not intend to update the code now (as embarrassing as it
might be).
## Known Issues
- Miniconda now uses the `conda activate` command line instead of `source activate`
- Miniconda now uses the `conda activate` command line instead of `source
activate`
## License
@ -81,15 +102,15 @@ Distributed under the MIT License. See `LICENSE` for more information.
Thomas A. Christensen II - [@MillironX](https://gab.com/MillironX)
Project Link: [https://github.com/MillironX/cowcalf-rumen-metagenomic-pipline](https://github.com/MillironX/cowcalf-rumen-metagenomic-pipline)
Project Link:
[https://github.com/MillironX/cowcalf-rumen-metagenomic-pipline](https://github.com/MillironX/cowcalf-rumen-metagenomic-pipline)
[hollinger-lab]: https://www.uwyo.edu/anisci/personnel-directory/wyoming-faculty-and-staff/hannah-cunningham-hollinger/index.html
[poster]: https://millironx.com/Academia#metagenomics
[arcc-servers]: https://www.uwyo.edu/arcc/
[slurm]: https://slurm.schedmd.com/overview.html
[qiime2-metadata]: https://docs.qiime2.org/2019.4/tutorials/metadata/
[R]: https://www.r-project.org/
[metaxa2]: https://microbiology.se/software/metaxa2/
[Miniconda]: https://conda.io/en/master/miniconda.html
[conda environment]: https://docs.qiime2.org/2019.4/install/native/#install-qiime-2-within-a-conda-environment
[hollinger-lab]:
https://www.uwyo.edu/anisci/personnel-directory/wyoming-faculty-and-staff/hannah-cunningham-hollinger/index.html
[poster]: https://millironx.com/Academia#metagenomics [arcc-servers]:
https://www.uwyo.edu/arcc/ [slurm]: https://slurm.schedmd.com/overview.html
[qiime2-metadata]: https://docs.qiime2.org/2019.4/tutorials/metadata/ [R]:
https://www.r-project.org/ [metaxa2]: https://microbiology.se/software/metaxa2/
[Miniconda]: https://conda.io/en/master/miniconda.html [conda environment]:
https://docs.qiime2.org/2019.4/install/native/#install-qiime-2-within-a-conda-environment
[Lmod]: https://lmod.readthedocs.io/en/latest/index.html