fragtk is a fast and efficient toolkit implemented in Rust for working with fragment files.
To install fragtk, please see the installation section below.
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>
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 according to the cell barcodes:
fragtk filter -f <fragments.tsv.gz> -c <barcodes.txt> | bgzip -c > filtered.tsv.gz
Clone the git repo:
git clone [email protected]:stuart-lab/fragtk.git
cd fragtk; cargo install --path .
Pre-compiled binaries are also available in the release.