fragtk: fragment file toolkit

fragtk is a fast and efficient toolkit implemented in Rust for working with fragment files.

To install fragtk, please see the installation section below.

Usage

Create region x cell matrix

A region x cell matrix can be created from a fragment file and a peak file:

fragtk matrix -f <fragments.tsv.gz> -b <peaks.bed> -c <cells.txt> -o <output>

Count fragments per cell barcode

Select cell barcodes from the fragment file according to their total count:

fragtk count -f <fragments.tsv.gz> -o <barcode_counts.tsv> -t <threshold> > barcodes.txt

Filter fragments

Filter fragments according to the cell barcodes:

fragtk filter -f <fragments.tsv.gz> -c <barcodes.txt> | bgzip -c > filtered.tsv.gz

Installation

Clone the git repo:

git clone git@github.com:stuart-lab/fragtk.git
cd fragtk; cargo install --path .

Pre-compiled binaries are also available in the release.