GfaPy: a flexible and extensible software library for handling sequence graphs in Python | Zendy

Giorgio Gonnella | Zendy; Stefan Kurtz | Zendy

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GfaPy: a flexible and extensible software library for handling sequence graphs in Python

Author(s) -

Giorgio Gonnella,

Stefan Kurtz

Publication year - 2017

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btx398

Subject(s) - python (programming language) , computer science , programming language , software , extensibility , parsing , scripting language , operating system

GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Here, we present GfaPy, a software package for creating, parsing and editing GFA graphs using the programming language Python. GfaPy supports GFA 1 and GFA 2, using the same interface and allows for interconversion between both formats. The software package provides a simple interface for custom record types, which is an important new feature of GFA 2 (compared to GFA 1). This enables new applications of the format.

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