gfatools for GFA (graphical fragment assembly) files – Jie Hua’s Bioinformatics Notes

Basic Information

GFA (Graphical Fragment Assembly) format is used for sequence assembly graphs. It was proposed by Prof. Dr. Heng Li in 2014. Here is his proposal: https://lh3.github.io/2014/07/19/a-proposal-of-the-grapical-fragment-assembly-format.

He updated this format in past 10 years to make it better. Here is his description about rGFA format: http://www.liheng.org/downloads/rGFA-GAF.pdf. Another one is https://github.com/lh3/gfatools/blob/master/doc/rGFA.md.

Shortly, GFA format is like SAM format, which is also developed by him. (I really like his work, that helped the academia a lot).

GFA is a simple TAB-dellimited text format consisting of 12 mandatory fields to represent reads aligned to a reference pan-genome graph: • Col 1–4: query name, length, start and end positions. • Col 5: the query strand relative to the mapping path in col 6. • Col 6: a stable graph path in the format matching the regular expression /([><][^\s><]+:\d+- \d+)+|([^\s><]+)/. The less or greater sign indicates the orientation of the segment. If a path consists of a single segment, coordinates can be omitted and its orientation is assumed to be forward “>”. • Col 7–9: total path length, start and end mapping positions on the forward strand of the path. • Col 10–12: number of matching bases, alignment block length and mapping quality

Each line may have tags as in the SAM format. CIGARs are stored in tags

Since the GFA format is so similar to SAM and PAF formats. I could use the R script that I wrote before to read and check those files. It may be better to use rust. I still need time to learn it.

Installation

git clone https://github.com/lh3/gfatools
cd gfatools
make
sudo cp gfatools /usr/local/bin/gfatools

Usage

Usage: gfatools <command> <arguments>
Commands:
  view        read a GFA file
  stat        statistics about a GFA file
  gfa2fa      convert GFA to FASTA
  gfa2bed     convert rGFA to BED (requiring rGFA)
  blacklist   blacklist regions
  bubble      print bubble-like regions (EXPERIMENTAL)
  asm         miniasm-like graph transformation
  sql         export rGFA to SQLite (requiring rGFA)
  ed          GWFA prefix alignment (for evaluation only)
  version     print version number

The most recent commit is https://github.com/lh3/gfatools/commit/c31be8a62efc6bdea4576029f7fbe84f345a6eed.