fpa Filter Pairwise Alignment

Filter output of all-against-all read mapping, you filter or select:

• internal match
• containment
• dovetails
• self matcing
• read name match against regex

All this filter can be revert.

For internal match, containment, dovetails definition go read algorithm 5 in minimap article

Rationale

Long Read mapping tools provides all match they found in read dataset, for many usage some of match aren't usfull, this programme provide some filter to remove it. This soft can be replace by a simple awk, bash, python, perl, {your favorite language}.

Requirements

• Rust in stable channel
• libgz
• libbzip2
• liblzma

Instalation

With cargo

If you have a rust environment setup you can run :

cargo install fpa_lr

With conda

fpa is avaible in bioconda channel

if bioconda channel is setup you can run :

conda install fpa

From source

git clone https://github.com/natir/fpa.git
cd fpa
git checkout v0.1

cargo build
cargo test
cargo install