nylander/fastp-cleaning

Clean fastq files with fastp

fastp-cleaning

• Last modified: tor okt 27, 2022 10:11
• Sign: nylander

Description

Filter fastq files using fastp.

Input

• gzipped paired-end Illumina .fastq.gz files. Example data (138M gzipped) can be downloaded here: https://owncloud.nrm.se/index.php/s/iT8SCXRwKTqUU3q

Output

• filtered .fq.gz files placed in a new output directory
• filtering reports (before/after)
• merged pair-end reads .fq.gz files (optional)
• fasta files from filtered fastq (optional)

Filtering steps

1. Filter on quality
2. Filter on length
3. Per read cutting per quality using a sliding window from front to tail
4. Adapters are automatically detected and trimmed
5. PCR-deduplicaiton (optional, by editing the config.yaml file)
6. Merging of paired-end read pairs (optional, by editing the config.yaml file)
7. Convert the filtered fastq filies to fasta (optional, by editing the config.yaml file)

Please see the fastp-manual for details on the filtering procedures.

---

How to run locally, without conda

1. Install
   • snakemake
   • fastp
   • seqtk
2. Clone the repository: git clone https://github.com/nylander/fastp-cleaning.git
3. Put input data (gzip-compressed paired-end Illumina fastq files) in folder fastp-cleaning/input
4. Review the fastp-cleaning/config/config.yaml and make sure input file name endings (currently _R1_001.fastq.gz), matches your input files, select the steps used by the pipeline, and change options for software used if needed.
5. Make sure your current working directory is fastp-cleaning
6. Test run snakemake -n
7. Run with snakemake --cores N (substitute N with the number of cores you wish to use)

How to run locally, with conda

1. Install
   • snakemake
   • conda
2. Clone the repository: git clone https://github.com/nylander/fastp-cleaning.git
3. Put input data (gzip-compressed paired-end illumina fastq files) in folder fastp-cleaning/input
4. Review the fastp-cleaning/config/config.yaml and make sure input file name endings (currently _R1_001.fastq.gz), matches your input files, select the steps used by the pipeline, and change options for software used if needed.
5. Make sure your current working directory is fastp-cleaning
6. Test run snakemake --use-conda -n
7. Run with snakemake --use-conda --cores N (substitute N with the number of cores you wish to use)

How to run on UPPMAX

Note: On rackham we are loading conda and snakemake (v.5) as modules. This can be done manually or using a script (rackham/scripts/init.sh). For convenience, we also start the run with the Makefile.

1. Log in to UPPMAX (rackham.uppmax.uu.se)
2. Clone the repository in a project folder: git clone https://github.com/nylander/fastp-cleaning.git
3. Edit the file fastp-cleaning/rackham/rackham.yaml to add your CPU-project account number. For example: sed -i -e 's/snic1234-56-789/snic2022-01-001/' rackham/rackham.yaml.
4. Add input files (use symbolic links to save space) to fastp-cleaning/input/
5. Review the fastp-cleaning/config/config.yaml and make sure input file-name endings (currently _R1_001.fastq.gz), matches your input files, select the steps used by the pipeline, and change options for software used if needed.
6. Start a screen session: screen -S fast-cleaning
7. Load modules: source rackham/scripts/init.sh
8. Test run: make slurm-test
9. Run: make slurm-run
10. Detach from the screen session (Ctrl+A, Ctrl+D).

TODO

• Add info on the filtering steps

Acknowledgements

The pipeline was heavily influenced by the stag-mwc pipeline.

License and copyright

Copyright (c) 2021, 2022 Johan Nylander

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.