sqz is a tool for compressing and decompressing path annotations in GFA files. It uses a modified version of the GFA-format containing Q- and Z-lines.
Use
sqz compress-full <GFA-FILE> > <COMPRESSED-GFA-FILE>to compress a GFA file and
sqz decompress <COMPRESSED-GFA-FILE> > <GFA-FILE>for decompression. For large GFA files take a look at
sqz compress-partial --helpUse
wget https://github.com/codialab/sqz/releases/download/v0.2.0/sqz
chmod +x sqzand make sqz available on your PATH to install it.
sqz is written in RUST and requires a working RUST build system (version >= 1.74.1) for installation. See here for more details.
git clone git@github.com:codialab/sqz.git
cd sqz
cargo build --releaseThe format of sqz is mostly based on the GFA format, but extended to include one new types of lines: Q-lines.
W-lines have been changed to allow the usage of identifiers from Q-lines.
A Q-line defines part of a compressed walk that can be used as part of other compressed walks.
| Column | Field | Type | Regexp | Description |
|---|---|---|---|---|
| 1 | RecordType |
Character | Q |
Record type |
| 2 | Name |
String | @[!-)+-<>-~][!-~]* |
Rule name |
| 3 | CompressedWalk |
String | ([><][!-;=?-~]+)+ |
Compressed Walk |
A Walk is defined as
<walk> ::= ( `>' | `<' <segId> )+where <segId> corresponds either to the identifier of a segment or the
identifier of a Q-line. A valid walk must exist in the graph. The identifier of
a Q-line starts with the character @
A walk line describes an oriented walk in the graph. It is only intended for a graph without overlaps between segments. Note that W-lines can not use jump connections (introduced in v1.2).
| Column | Field | Type | Regexp | Description |
|---|---|---|---|---|
| 1 | RecordType |
Character | W |
Record type |
| 2 | SampleId |
String | [!-)+-<>-~][!-~]* |
Sample identifier |
| 3 | HapIndex |
Integer | [0-9]+ |
Haplotype index |
| 4 | SeqId |
String | [!-)+-<>-~][!-~]* |
Sequence identifier |
| 5 | SeqStart |
Integer | \*|[0-9]+ |
Optional Start position |
| 6 | SeqEnd |
Integer | \*|[0-9]+ |
Optional End position (BED-like half-close-half-open) |
| 7 | CompressedWalk |
String | ([><][!-;=?-~]+)+ |
Compressed Walk |
For a haploid sample, HapIndex takes 0. For a diploid or polyploid sample,
HapIndex starts with 1. For two W-lines with the same
(SampleId,HapIndex,SeqId), their [SeqSart,SeqEnd) should have no
overlaps. A Walk is defined as
<walk> ::= ( `>' | `<' <segId> )+where <segId> corresponds either to the identifier of a segment or the
identifier oft a Q-line. A valid walk must exist in the graph.
S s11 ACCTT
S s12 TC
S s13 GATT
L s11 + s12 - 0M
L s12 - s13 + 0M
L s11 + s13 + 0M
Q @q1 >s11<s12
W NA12878 1 chr1 0 11 >@q1>s13Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/LIPIcs.WABI.2025.14