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ABySS File Formats
Sequence overlap graph in ABySS adj (adjacency) format.
See the ABySS dot file format for a description of a sequence overlap graph.
Example:
23 44 198 ; 3193- 56- [d=-23] ; 3681-
25 30 1045 ; 3983- 1794- [d=-28] 2808+ [d=-28] 3136- [d=-28] ; 2699+ 4758+
27 54 175 ; 1255+ 4657- ;
28 51 3854 ; 875+ 3725- ; 1314- [d=-21]
29 73 1151 ; 3015+ ; 2199+
30 34 4896 ; 229- 4236+ [d=-26] 4060+ [d=-24] ; 2091+ 4267+
31 58 2483 ; 1454+ [d=-28] ; 3453+ [d=-28]
32 33 530 ; 2566- ; 3453+ [d=-28]
The .adj files generated by ABySS describe the sequence overlap graph at each stage of an assembly. In the sequence overlap graph, each vertex represents a sequence (e.g. a contig) and each edge represents a perfect overlap between the ends of two sequences. In most cases, the length of the sequence overlap is k - 1 bases.
An .adj file consists of 3 fields per line, separated by semicolons (';').
The first field (e.g. "28 51 3854") provides information about the subject sequence and consist of 3 parts: <SEQ_ID> <SEQ_LEN> <KMERS>, where SEQ_ID is a unique identifier for the sequence assigned by ABySS, SEQ_LEN is the length of the sequence in bases, and KMERS is the number of KMERS that mapped to the sequence during assembly (i.e. the sum of kmer multiplicities for each kmer in the sequence.)
The second and third fields (e.g. "3193- 56- [d=-23]", "3681-") list the SEQ_ID of sequences that overlap the subject sequence. Each field consists of a list of whitespace-separated SEQ_ID, each of which has a + or - suffix to indicate the sense of the sequence that produces the overlap. The +/- sense of a given sequence is determined by the form it takes in the FASTA file corresponding to the .adj file. Using the naming conventions of the ABySS output files, this correspondence should usually be clear (e.g. "myassembly-1.adj" corresponds to "myassembly-1.fa"). The sense of the sequence listed in the FASTA file is considered to be the + sense. By default, the length of the overlap between two sequences is assumed to be k - 1 bases. If this not the case, an additional distance specifier (e.g. "[d=-23]") must be inserted following the SEQ_ID to indicate that the overlap is of a different length. A negative distance value indicates the overlap size in bases, whereas a positive distance indicates a gap size in bases.
It is important to note that the order of the second and third fields is exactly the opposite of what one would expect; the second field lists sequences that overlap the subject sequence on the right side and the third field lists sequences that overlap the subject sequence on the left side.
The .adj format is a ABySS-specific format for describing graphs that should preferably be replaced by the more standard .dot format.
NCBI GenBank Accessioned Golden Path
Sequence overlap graph in SGA ASQG format
ABySS can read and write ASQG files.
Tabular data in Comma-separated values format
Distance estimates in ABySS dist format (similar to adj format)
Distance estimate graph in Graphviz dot format
This file format is an extensions of the ABySS dot file format for sequence overlap graphs.
| Edge property | Description |
|---|---|
| d | Distance (bp) |
| e | Estimated error (bp) |
| n | Number of supporting fragments |
The estimated distance from A+ to B+ is 100 bp with an estimated error of 5 bp and is supported by 10 read pairs:
"A+" -> "B+" [d=100 e=5 n=10]Sequence overlap graph in Graphviz dot format
As a sequence overlap graph is primarily a graph, ABySS uses an existing graph file format, the GraphViz DOT file format. The GraphViz DOT syntax is well defined and implemented by a number of existing graph tools. Below is described how ABySS represents a sequence overlap graph using a subset of the GraphViz DOT language.
- Sequences are represented by vertices and overlaps by directed edges.
- A sequence is represented by two vertices: one vertex for the sequence itself and one for its reverse complement, which are named "A+" and "A-" respectively for a sequence named "A".
- A directed edge represents an overlap of two sequences.
indicates that a suffix of A matches a prefix of B.
"A+" -> "B+"
Consider the following simple graph of four sequences (vertices) and three overlaps (edges).
A --> B
\
\
C --> D
The DOT graph is:
digraph g {
"A+" -> "B+"
"A+" -> "D+"
"C+" -> "D+"
}When the contig A overlaps the reverse complement of B, it's shown like so:
"A+" -> "B-"Just as every vertex was a twin, every edge has a twin. The existence of an edge (u, v) implies the existence of an edge (v-, u-), where x- denotes the reverse complement of x.
The following pairs of edges are equivalent:
"A+" -> "B+" "B-" -> "A-"
"C+" -> "D-" "D+" -> "C-"
"E-" -> "F+" "F-" -> "E+"Vertices and edges may be augmented with properties. For example, The length of the contig A is 100 bp:
"A+" [l=100]The sequences "A+" and "B+" overlap by 100 bp.
"A+" -> "B+" [d=-100]ABySS represents an overlap with a negative distance and a gap with a positive distance. In this manner, the length of a path through the graph is the sum of the vertex lengths and edge distances.
The type (integer, float or string) of a property is evident from its format.
-
[l=100]is an integer -
[c=3.5]is a float -
[s="ABC"]is a string
For a De Bruijn graph where all overlaps are exactly k-1 bp, a default edge property may be used. e.g. both overlaps below are 31 bp.
digraph g {
edge [d=-31]
"A+" -> "B+"
"B+" -> "C+"
}The contig sequences are stored in a separate indexed FASTA file (.fai).
Using a standard file format has the advantage of giving immediate access to existing tools. For example...
- Render the graph for visualization
dot -Tpng in.dot -o out.png
- Count the number of vertices and edges
gc g.dot
- Count the number of connected components
gc -c g.dot
- Separate the connected components into separate files
ccomps -x in.dot -o out.dot
- Remove any contigs with less than 5 coverage (where c is the
coverage property)
gvpr -i 'N[c>=5]' in.dot >out.dot
- Calculate the distance from a source vertex to all other vertices
dijkstra "A+" in.dot >out.dot
ABySS includes a tool, abyss-todot, to convert between sequence
overlap graph formats, including SGA ASQG, SAM and
ABySS ADJ.
Contig and scaffold sequences in FASTA format
An index of sequences in FASTA format
| Column | Description |
|---|---|
| 1 | Name of the sequence |
| 2 | Length of the sequence |
| 3 | Offset of the first base in the file |
| 4 | Number of bases in each line |
| 5 | Number of bytes in each line |
A histogram of the fragment size distribution in tab-separated values format, without a header
| Column | Description |
|---|---|
| 1 | Fragment size |
| 2 | Count |
- Positive fragment sizes are oriented forward-reverse (FR).
- Negative fragment sizes are oriented reverse-forward (RF).
Reports in Markdown format
Scaffolds in ABySS PATH format
If the line is composed of a single identifier, the specified contig is removed from the assembly. Otherwise, the first column of the line is the ID of the new scaffold, and the remainder of the line is a sequence of contig IDs and their orientation.
Reads aligned to contig/scaffold sequences in Sequence Alignment/Map format
Example:
@SQ SN:5105 LN:122
@SQ SN:5106 LN:92
@SQ SN:5107 LN:186
* 161 4 1 32 6S32M63S 77 1 77 * *
* 161 4 1 32 40S32M29S 215 1 134 * *
* 129 4 1 32 69S32M 358 1 50 * *
* 161 4 1 31 31M70S 1390 1 34 * *
* 161 4 1 32 6S32M63S 1390 1 46 * *
* 161 4 1 32 6S32M63S 77 1 59 * *
* 161 4 1 32 6S32M63S 77 1 55 * *
* 177 4 1 32 58S32M11S 147 1 13 * *
* 161 4 1 30 13S30M58S 77 1 60 * *
The SAM format is used by ABySS to describe alignments of reads to assembled sequences at different stages of the assembly. As of ABySS version 1.3.8, the reads are aligned to the assembled sequences twice: once during the construction of the contigs, and once during the construction of the scaffolds.
By default, ABySS omits field 1 (QNAME, the ID of the aligned sequence), field 10 (SEQ, the aligned sequence), and field 11 (QUAL, the quality string of the aligned sequence) from any generated SAM data, placing a * in these fields instead. This is done because the fields are not needed by ABySS to calculate distances estimates, and omitting the fields greatly reduces the overall size of the SAM data. (To generate SAM data that contains all of the fields, ABySS may be compiled using the --enable-samseqqual option for configure.)
The ABySS assembly pipeline does not generate any output SAM files by default, because the files tend to be very large. Instead, ABySS streams the SAM data through a Unix command pipeline to generate the distance estimates that are used to link contigs and scaffolds. Only the distance estimates are saved to disk (.dist and .dist.dot files). However, an ABySS user may force generation of output SAM files by specifying the "pe-sam" and/or "mp-sam" targets on the "abyss-pe" commandline, e.g.
abyss-pe name=myassembly k=40 in='read1.fastq read2.fastq' pe-sam mp-sam scaffolds
The "pe-sam" and "mp-sam" targets will generate the files myassembly-3.sam.gz and myassembly-6.sam.gz, respectively. There are also "pe-bam" and "mp-bam" targets if the user wishes to generate equivalent BAM (compressed SAM) files. See the abyss-pe man page for more info.
Statistics of contig/scaffold contiguity in TSV, CSV and Markdown formats
Tabular data in tab-separated values format, including a one-line header