https://github.com/lh3/gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats
https://github.com/lh3/gfatools

bioinformatics genome-graph genomics

Last synced: 26 days ago
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Tools for manipulating sequence graphs in the GFA and rGFA formats

• Host: GitHub
• URL: https://github.com/lh3/gfatools
• Owner: lh3
• Created: 2019-02-07T16:27:36.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-02-20T15:29:14.000Z (10 months ago)
• Last Synced: 2024-05-08T22:00:55.378Z (7 months ago)
• Topics: bioinformatics, genome-graph, genomics
• Language: C
• Homepage:
• Size: 542 KB
• Stars: 197
• Watchers: 16
• Forks: 18
• Open Issues: 17
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

        
## Getting Started

```sh

git clone https://github.com/lh3/gfatools

cd gfatools && make

# Extract a subgraph

./gfatools view -l MTh4502 -r 1 test/MT.gfa > sub.gfa

# Convert GFA to segment FASTA

./gfatools gfa2fa test/MT.gfa > MT-seg.fa

# Convert rGFA to stable FASTA or BED

./gfatools gfa2fa -s test/MT.gfa > MT.fa

./gfatools gfa2bed -m test/MT.gfa > MT.bed

```

## Introduction

gfatools is a set of tools for manipulating sequence graphs in the GFA or the

[rGFA][rGFA] format. It has implemented parsing, subgraph and conversion to

FASTA/BED. More functionality may be added in future.

[rGFA]: https://github.com/lh3/gfatools/blob/master/doc/rGFA.md