Image: github.com · ampliscan — sort sequencing reads into per-sample bins by their barcodes
ampliscan, a barcode sorter for pooled amplicon sequencing reads
A plant biology researcher built a Python tool with a GUI to sort sequencing reads by barcode, working through it with Claude Code.
Credits
- Reddit poster Dismal-Surround-1449 Source ↗
- Repository account Ayushmania2002 Source ↗
Earliest dated source:
The full story
A plant biology researcher needed to sort pooled amplicon sequencing reads into per-sample files using barcodes on custom primers, and had never built a Python package before. With Claude Code they built ampliscan, which finds anchor sequences, reads the barcode beside them and bins each read, with a CLI and a tkinter GUI.
It was tested on a real run of 6.6 million read pairs, with 85.8% assigned. Claude helped find that multiprocessing slowed it because gzip I/O was the bottleneck, and a faster gzip library fixed that. It is published on PyPI.
How it was done
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Sources
From a short post by the maker, so the details are as they tell them.
- Reddit: Built a bioinformatics tool with Claude Code: ampliscan, a barcode demultiplexer with a GUIReddit poster: Dismal-Surround-1449Posted
The maker's reply in r/ClaudeAI's showcase thread.
If it disappears: archived copy of Reddit: Built a bioinformatics tool with Claude Code: ampliscan, a barcode demultiplexer with a GUI (opens in a new tab)
- The code: github.comRepository account: Ayushmania2002
The project on GitHub.