gfa2gff

gfa2gff is a command-line tool that converts a GFA (Graphical Fragment Assembly) file representing a compacted de Bruijn graph into a GFF3 annotation file.
Each segment in the GFA graph becomes one feature in the GFF file. This makes it possible for downstream tools to view and analyze the graph directly in genomic coordinates.

It is compatible with graphs produced by tools such as Bifrost, GGCAT, TwoPaCo, BCALM2, Cuttlefish2 and any other that generate GFA representations of compacted de Bruijn graphs.

What this means:

Say you have a genome with three chromosomes.
Two of them (chr1 and chr2) differ by a single base in the middle (A ↔ T), while chr3 is the same as chr1 but with an N inserted.

example.fa

>chr1
GATACAT
>chr2
GATTCAT
>chr3
GATNACAT

Its compacted de Bruijn graph (without considering canonical unitigs) for k=3 is the following:

         ┌───(2) ATACA───┐
(1) GAT──┤               ├──(4) CAT
         └───(3) ATTCA───┘

The GFF output by gfa2gff is shown below. Here:

• ID= is the ID of the node in the GFA.
• genome= is the name of the FASTA file it comes from (example.fa).
• substr= is present when the string is a substring of the node.
  In this case, the string ACA is a substring of node 2, from position 3 to 5. (These positions are 1-based index and both inclusive, like in the GFF).

In chr3 the 4th base (N) is not represented, since it is not an A/C/G/T character and most compacted de Bruijn graph tools ignore such regions.

The #num represents an incremental 1-based number given to each fasta file. It guarantess that seqnames from different genomes remain different afterwards. It can be deactivated with --no_distinct_seqname.

##gff-version 3.1.26
##sequence-region chr1 1 7
##sequence-region chr2 1 7
##sequence-region chr3 1 8
chr1#1	gfa2gff	SO:0000856	1	3	.	+	.	ID=1;genome=example
chr1#1	gfa2gff	SO:0000856	2	6	.	+	.	ID=2;genome=example
chr1#1	gfa2gff	SO:0000856	5	7	.	+	.	ID=4;genome=example
chr2#1	gfa2gff	SO:0000856	1	3	.	+	.	ID=1;genome=example
chr2#1	gfa2gff	SO:0000856	2	6	.	+	.	ID=3;genome=example
chr2#1	gfa2gff	SO:0000856	5	7	.	+	.	ID=4;genome=example
chr3#1	gfa2gff	SO:0000856	1	3	.	+	.	ID=1;genome=example
chr3#1	gfa2gff	SO:0000856	5	7	.	+	.	ID=2;genome=example;substr=(3,5)
chr3#1	gfa2gff	SO:0000856	6	8	.	+	.	ID=4;genome=example

Install

Dependencies

• C++17
• OpenMP
• zlib

Clone the repository and build:

git clone https://github.com/lucaparmigiani/gfa2gff
cd gfa2gff
make

Run

Basic usage:

gfa2gff <k> <graph.gfa[.gz]> <genome.fasta> [more.fasta ...] [options]

The GFA input may be plain text or gzip-compressed (.gfa.gz).

Options:

• -t, --threads <N>: number of threads (default: all available cores)
• -a, --ignore_absent_kmers: ignore when a k-mer is not found in the compacted de Bruijn graph

Example

Run with three genomes:

gfa2gff 11 example/graph.gfa example/a.fa example/b.fa example/c.fa > graph.gff

Output:

##gff-version 3.1.26
##sequence-region A#1 1 77
##sequence-region B#2 1 137
##sequence-region C#3 1 206
A#1	gfa2gff	SO:0000856	1	11	.	+	.	ID=10;genome=a
A#1	gfa2gff	SO:0000856	2	12	.	+	.	ID=11;genome=a
A#1	gfa2gff	SO:0000856	3	13	.	+	.	ID=12;genome=a
A#1	gfa2gff	SO:0000856	4	14	.	-	.	ID=12;genome=a
A#1	gfa2gff	SO:0000856	5	15	.	+	.	ID=13;genome=a
A#1	gfa2gff	SO:0000856	6	16	.	-	.	ID=13;genome=a
...
B#2	gfa2gff	SO:0000856	1	11	.	-	.	ID=15;genome=b
B#2	gfa2gff	SO:0000856	2	14	.	+	.	ID=3;genome=b
B#2	gfa2gff	SO:0000856	5	16	.	+	.	ID=2;genome=b
B#2	gfa2gff	SO:0000856	7	17	.	-	.	ID=14;genome=b
B#2	gfa2gff	SO:0000856	8	18	.	-	.	ID=15;genome=b
...
C#3	gfa2gff	SO:0000856	126	137	.	+	.	ID=2;genome=c
C#3	gfa2gff	SO:0000856	128	138	.	-	.	ID=14;genome=c
C#3	gfa2gff	SO:0000856	129	139	.	-	.	ID=15;genome=c
C#3	gfa2gff	SO:0000856	130	142	.	+	.	ID=3;genome=c
C#3	gfa2gff	SO:0000856	133	144	.	+	.	ID=2;genome=c
C#3	gfa2gff	SO:0000856	135	145	.	-	.	ID=14;genome=c
C#3	gfa2gff	SO:0000856	136	146	.	-	.	ID=15;genome=c
C#3	gfa2gff	SO:0000856	137	156	.	+	.	ID=4;genome=c
C#3	gfa2gff	SO:0000856	165	182	.	+	.	ID=9;genome=c;substr=(3,20)
C#3	gfa2gff	SO:0000856	189	206	.	-	.	ID=9;genome=c;substr=(3,20)