[PPoPP24] AGAThA: Fast and Efficient GPU Acceleration of Guided Sequence Alignment for Long Read Mapping

!!! Important Notice !!!

This repository is currently undergoing a major update.

It is strongly recommended to revisit this repository after a new release is made.

Getting Started

1. Environment Setup with Docker

cd docker
bash build.sh
bash launch.sh

2. Datasets & Building AGAThA

A sample dataset can be found in dataset/. AGAThA can be built by running the following code:

cd AGAThA
bash build.sh
cd ..

AGAThA Details

AGAThA was built on top of GASAL2.

1. AGAThA Options

Using AGAThA.sh, we can use the following options for AGAThA.

-m  the match score
-x  the mismatch penatly
-q  the gap open penalty
-r  the gap extension penalty
-z  the termination threshold
-w  the band width in the score table

2. AGAThA Input

AGAThA requires two datasets as input;

• a fasta file with reference sequences labeled with sequence indices
• a fasta file with query sequences labeled with sequences indices Both files should follow the format below:

>>> 1
ATGCN...
>>> 2
TCGGA...

Fasta files can be downloaded from various sources such as GenBank or projects such as Genome in a Bottle.