Hi all,
I'd like to share a modular and transparent bash-based pipeline I’ve developed for pre-processing ddRADseq Illumina paired-end reads. It handles everything from adapter removal to demultiplexing and PCR duplicate filtering — all using standard tools like cutadapt, seqtk, and shell scripting.
The pipeline performs:
It is fully documented, lightweight, and designed for reproducibility.
I created it for my own ddRAD projects, but I believe it might be useful for others working with RAD/GBS data too.
🔗 GitHub repository: https://github.com/rafalwoycicki/ddRADseq_reads
The scripts are especially helpful for people who want to avoid complex pipeline wrappers and prefer clear, customizable shell workflows.
Feedback, suggestions, and test results are very welcome!
Let me know if you'd like to discuss use cases or improvements.
Best,
Rafał
I'd like to share a modular and transparent bash-based pipeline I’ve developed for pre-processing ddRADseq Illumina paired-end reads. It handles everything from adapter removal to demultiplexing and PCR duplicate filtering — all using standard tools like cutadapt, seqtk, and shell scripting.
The pipeline performs:
- Adapter trimming with quality filtering (cutadapt)
- Demultiplexing based on inline barcodes (cutadapt again)
- Restriction site filtering + rescue of partially matching reads
- Pairwise read deduplication using custom logic with DBR region with seqtk + awk
- Final read shortening
It is fully documented, lightweight, and designed for reproducibility.
I created it for my own ddRAD projects, but I believe it might be useful for others working with RAD/GBS data too.
🔗 GitHub repository: https://github.com/rafalwoycicki/ddRADseq_reads
The scripts are especially helpful for people who want to avoid complex pipeline wrappers and prefer clear, customizable shell workflows.
Feedback, suggestions, and test results are very welcome!
Let me know if you'd like to discuss use cases or improvements.
Best,
Rafał
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