In the paper Petrisnake, an improved computational pipeline for bacterial single-cell RNA-seq , two secondary analysis bioinformatic pipelines for data from the PETRI-seq protocol (Blattman et al. 2020) are compared and benchmarked. One of these pipelines is the original PETRI-seq pipeline (Blattman et al. 2020 and Blattman et al. 2024, available at https://github.com/tavalab/PETRI-seq-persistence) and the other is Petrisnake which is introduced by this paper (available at https://github.com/yaccos/Petrisnake and https://workflowhub.eu/workflows/2081).

The benchmarking was conducted on a PETRI-seq sample of exponential phase Escherichia coli cells (Yan et al. 2024), available at NCBI under accession under SRR28148450. Because of size considerations, this raw sequence data are not attached to this repository and must hence be downloaded separately if you want to re-run the benchmarks.

This repository contains the output data files such as gene count matrices and UMI count tables from the two pipelines, in addition to the logs generated. These files are kept as-is with selected figure provided in archive-friendly formats.

For comparing the results of the two pipelines, the paper includes a multi-panel figure comparing the outputs of the two pipelines (comparison.pdf). This repository contains an R script which uses the output data from the pipelines and generates the said figure.

Petrisnake, 2.0

PETRI-seq pipeline, v2