gfalign

Graph alignment and analysis.

Prerequisites

An installation of conda is required.

Installation

To install run git clone https://github.com/vgl-hub/gfalign.git --recursive and make -j in the gfalign folder.

Usage

gfalign [options] [tool] [arguments]

Gfalign uses a graph-aware aligner, e.g. GraphAligner, to align reads to an assembly graph and then evaluates the graph based on the alignment.

First generate an alignment, e.g.:

gfalign -p hifi align -f testFiles/random2.reads.fq -g testFiles/random2.gfa -a aln.gaf

Then compute statistics:

gfalign eval -g aln.gaf

Or decorate the graph with information from the alignment:

gfalign eval -g aln.gaf -f testFiles/random2.gfa -o newGFA.gfa

To check out all tool and options available use gfalign -h.

How to cite

If you use gfalign in your work, please cite:

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs

Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristo Gallardo, Alice Giani, Olivier Fedrigo, Erich D. Jarvis

doi: https://doi.org/10.1093/bioinformatics/btac460