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Bagpiper & BenchDrop-seq: a microfluidics-free workflow for benchtop single-cell long-read RNA sequencing

Year: 2026

Type: software

Abstract: Source code for BenchDrop-seq, a microfluidics-free workflow for benchtop single-cell long-read RNA sequencing. bagpiper-0.1.0 is the Bagpiper pipeline (Rust, MIT license) that recovers cell barcodes from long reads and quantifies isoforms and genes per cell, tag 0.1.0 of https://github.com/avisrilab/bagpiper, the version used for every analysis in the manuscript. benchdrop_paper is the analysis code for the figures, tables and benchmarks, including the barcoded single-cell read simulator, commit 6787f7f of https://github.com/avisrilab/benchdrop_paper.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.22731585

Authors: Srivastava, Avi, Bregman, Jamie, Nichols, Calen, Ramisetti, Rajeev

Institution: The Wistar Institute

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W7213332901

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