Python 2021-10-26

Fasta to GFA

Fasta to GFA is a small python script used for converting Fasta files to GFA files for visualization in Bandage. This is just for visualization, since no coverage or linking information is available from a Fasta file. This also means that there are no circular fragments in these GFA files.

This can be used in cases like polishing assembled third generation sequencing data with Medaka and Racon after a Flye assembly. Since Medaka and Racon do not provide a GFA output file, but Flye does.

This tool makes it easy to visualize these polished assemblies and have a look at the different contigs.

The tool is available on our github.


About AuthorSenior Author

Hi, my name is Cedric Hermans. I'm a lecturer at the bioinformatics department of Howest. I am also a researcher at the BiKC knowledge centre. I am mainly involved in databases and data management, AI/Machine learning, Rshiny applications and python scripts.