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

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Abstract

Summary:

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.

Availability and implementation:

GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip.

Contact:

gonnella@zbh.uni-hamburg.de

Supplementary information:

Supplementary data are available at Bioinformatics online.

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