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deepsort-rs

Introduction

deepsort is a Rust-based command-line tool to quickly sort gzipped FASTQ files. It takes the demultiplexed calls from the deeplexicon package and quickly sorts the reads.

deepsort reads a barcode file, maps read IDs to barcodes, and then sorts and writes reads from gzipped FASTQ files into new gzipped files based on their barcodes.

Installation

To install deepsort, you need to have Rust and Cargo installed on your system. If you don't have Rust installed, follow the instructions on Rust's official website.

git clone https://github.com/rnabioco/deepsort-rs

cd deepsort-rs

cargo install --path .

Usage

To use deepsort, navigate to the cloned directory and run the following command:

deepsort <barcode_file> <fastq_folder> [output_folder]
  • <barcode_file>: The path to the barcode demux file output from deeplexicon.
  • <fastq_folder>: The directory containing gzipped FASTQ files.
  • [output_folder]: (Optional) The directory where the output files will be saved. If not specified, files will be saved in the current directory.