Table 3.

Graphical fragment assembly format (GFA)

Line	Comment	Fixed fields
H	Header	N/A
S	Segment	segName,segSeq
L	Overlap	segName1, segOri1, segName2, segOri2, CIGAR

GFA is a line-based TAB-delimited format. Each line starts with a single letter determining the interpretation of the following TAB-delimited fields. In GFA, segment refers to a read or a unitig. A line start with ‘S’ gives the name and sequence of a segment. When the sequence is not available, it can be a star ‘*’. Overlaps between segments are represented in lines starting with ‘L’, giving the names and orientations of the two segments in an overlap. The last field ‘CIGAR’ on an ‘L’-line describes the detailed alignment of the overlap if available. In addition to the types of lines in the table, GFA may contain other line types starting with different letters. Each line may optionally have additional SAM-like typed key-value pairs.