GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats

GFAKluge is a set of command line utilities and a C++ library for parsing and manipulating the Graphical Fragment Assembly (GFA) format. Genome assembly algorithms often use graph structures to represent relationships between reads during the assembly process. Such information is typically thrown away when assemblies are converted to FASTA files of contig sequences. Previous attempts to convey graph information did not gain widespread acceptance because there were no standard representations that were easily parsed and extensively used. The Graphical Fragment Assembly (GFA) format was proposed as a way to encode the graph structure of an assembly in a human-readable text format (Li, 2014). GFA aims to provide a single format for interchange between software for assembly, scaffolding, assessment and visualization. Such programs are often written in high-performance programming languages such as C or C++. GFAKluge facilitates interprogram exchange by providing a high-level C++ API for developers and a set of command line tools for users. We hope the availability of an open-source, easily extensible API will encourage software developers to consider adding support for GFA to their bioinformatics programs. Homepage: https://github.com/edawson/gfakluge License: MI