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

Compute QC metrics

Compute scATAC-seq quality control metrics per cell:

fragtk qc -f <fragments.tsv.gz> -o <outfile.tsv.gz> <--gff <genes.gff3.gz> |--bed <tss.bed.gz>>

Installation

Using cargo

cargo install fragtk

From GitHub

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

Pre-compiled binaries are also available in the release.

Man Pages

The tool includes man pages (documentation) that can be generated and installed after installation:

# generate manpages
fragtk generate-manpages --outdir /tmp/fragtk-man

# install man pages (requires sudo)
# note that this path may be different on different systems
sudo cp /tmp/fragtk-man/*.1 /usr/local/share/man/man1/

# on linux, update the manual page cache by running mandb
sudo mandb

Once installed, you can view the documentation with:

man fragtk # main command documentation
man fragtk-matrix # matrix subcommand documentation
man fragtk-count # count subcommand documentation
man fragtk-filter # filter subcommand documentation

Alternatively, you can view the man pages directly without installation:

man /tmp/fragtk-man/fragtk.1