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Graphical Fragment Assembly (GFA) Format Specification
The GFA Format Specification Working Group
2016-09-15

The master version of this document can be found at
https://github.com/GFA-spec/GFA-spec

The GFA Format Specification

The purpose of the GFA format is to capture sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology.

The GFA format is a tab-delimited text format for describing a set of sequences and their overlap. The first field of the line identifies the type of the line. Header lines start with H. Segment lines start with S. Link lines start with L. A containment line starts with C. A path line starts with P.

Terminology

  • Segment a continuous sequence or subsequence.
  • Link an overlap between two segments. Each link is from the end of one segment to the beginning of another segment. The link stores the orientation of each segment and the amount of basepairs overlapping.
  • Containment an overlap between two segments where one is contained in the other.
  • Path an ordered list of oriented segments, where each consecutive pair of oriented segments are supported by a link record.

Line structure

Each line in GFA has tab-delimited fields and the first field defines the type of line. The type of the line defines the following required fields. The required fields are followed by optional fields.

Type Description
# Comment
H Header
S Segment
L Link
C Containment
P Path

Optional fields

All optional fields follow the TAG:TYPE:VALUE format where TAG is a two-character string that matches /[A-Za-z][A-Za-z0-9]/. Each TAG can only appear once in one line. A TAG containing lowercase letters are reserved for end users. A TYPE is a single case-sensitive letter which defines the format of VALUE.

Type Regexp Description
A [!-~] Printable character
i [-+]?[0-9]+ Signed integer
f [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? Single-precision floating number
Z [ !-~]+ Printable string, including space
J [ !-~]+ JSON, excluding new-line and tab characters
H [0-9A-F]+ Byte array in hex format
B [cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+ Array of integers or floats

For type B, array of integers or floats, the first letter indicates the type of numbers in the following comma separated array. The letter can be one of cCsSiIf, corresponding to int8_t (signed 8-bit integer), uint8_t (unsigned 8-bit integer), int16_t, uint16_t, int32_t, uint32_t and float, respectively.

# Comment line

Comment lines begin with # and are ignored.

Required fields

Column Field Type Regexp Description
1 RecordType Character # Record type

H Header line

Required fields

Column Field Type Regexp Description
1 RecordType Character H Record type

Optional fields

Tag Type Description
VN Z Version number

S Segment line

Required fields

Column Field Type Regexp Description
1 RecordType Character S Record type
2 Name String [!-)+-<>-~][!-~]* Segment name
3 Sequence String \*|[A-Za-z=.]+ Optional nucleotide sequence

Segment names must not contain whitespace characters nor start with * or = nor contain the strings +, and -,. All other printable ASCII characters are allowed. Names are case sensitive.

The Sequence field is optional and can be *, meaning that the nucleotide sequence of the segment is not specified. When the sequence is not stored in the GFA file, its length may be specified using the LN tag, and the sequence may be stored in an external FASTA file.

Optional fields

Tag Type Description
LN i Segment length
RC i Read count
FC i Fragment count
KC i k-mer count
SH H SHA-256 checksum of the sequence
UR Z URI or local file-system path of the sequence. If it does not start with a standard protocol (e.g. ftp), it is assumed to be a local path.

L Link line

Links are the primary mechanism to connect segments. Links connect oriented segments. A link from A to B means that the end of A overlaps with the start of B. If either is marked with -, we replace the sequence of the segment with its reverse complement, whereas a + indicates the segment sequence is used as-is.

The length of the overlap is determined by the CIGAR string of the link. When the overlap is 0M the B segment follows directly after A. When the CIGAR string is *, the nature of the overlap is not specified.

Required fields

Column Field Type Regexp Description
1 RecordType Character L Record type
2 From String [!-)+-<>-~][!-~]* Name of segment
3 FromOrient String +|- Orientation of From segment
4 To String [!-)+-<>-~][!-~]* Name of segment
5 ToOrient String +|- Orientation of To segment
6 Overlap String \*|([0-9]+[MIDNSHPX=])+ Optional CIGAR string describing overlap

The Overlap field is optional and can be *, meaning that the CIGAR string is not specified.

Optional fields

Tag Type Description
MQ i Mapping quality
NM i Number of mismatches/gaps
RC i Read count
FC i Fragment count
KC i k-mer count
ID Z Edge identifier

C Containment line

A containment line represents an overlap between two segments where one (the Contained segment) is contained in the other (the Container segment). The Pos field stores the leftmost position of the contained segment in the container segment in its forward orientation (i.e. before this is oriented according to the ContainerOrient sign).

Example

The following line describes the containment of segment 2 in the reverse complement of segment 1, starting at position 110 of segment 1 (in its forward orientation).

C  1 - 2 + 110 100M

Required fields

Column Field Type Regexp Description
1 RecordType Character C Record type
2 Container String [!-)+-<>-~][!-~]* Name of container segment
3 ContainerOrient String +|- Orientation of container segment
4 Contained String [!-)+-<>-~][!-~]* Name of contained segment
5 ContainedOrient String +|- Orientation of contained segment
6 Pos Integer [0-9]* 0-based start of contained segment
7 Overlap String \*|([0-9]+[MIDNSHPX=])+ CIGAR string describing overlap

Optional fields

Tag Type Description
RC i Read coverage
NM i Number of mismatches/gaps
ID Z Edge identifier

P Path line

Required fields

Column Field Type Regexp Description
1 RecordType Character P Record type
2 PathName String [!-)+-<>-~][!-~]* Path name
3 SegmentNames String [!-)+-<>-~][!-~]* A comma-separated list of segment names and orientations
4 Overlaps String \*|([0-9]+[MIDNSHPX=])+ Optional comma-separated list of CIGAR strings

The Overlaps field is optional and can be *, in which case the CIGAR strings are determined by fetching the CIGAR string from the corresponding link records, or by performing a pairwise overlap alignment of the two sequences.

Optional fields

None specified.

Example

H	VN:Z:1.0
S	11	ACCTT
S	12	TCAAGG
S	13	CTTGATT
L	11	+	12	-	4M
L	12	-	13	+	5M
L	11	+	13	+	3M
P	14	11+,12-,13+	4M,5M

The resulting path is:

11 ACCTT
12  CCTTGA
13   CTTGATT
14 ACCTTGATT