Sequence Read Format (SRF)

SRF is a generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. Hence, the format has sufficient flexibility to store data from current and future DNA sequencing technologies at minimal cost of implementation.

Benefits include a single input file format for all downstream applications and a read lookup index enabling downstream formats to reference reads without duplication of all of the read specific information.

This format has been developed as an open collaborative effort between many groups and individuals.

The mailing list for the group is maintained here.

Releases

Versioning Convention

This convention was adopted at v1.3 (first stable release) and may not apply to earlier releases.

Version format a.b.c

a - incremented on a major change to the format e.g. the addition of new block type.
b - incremented on a minor change to the format.
c - incremented for a document change that does not modify the format.

Hence, the documents v1.3 and v1.3.1 both refer to the same format, v1.3.

Status

Version 1.3 of the specification is stable.

The document describing v1.3 is available here as a single HTML file.

A draft revision of the v1.3 document (v1.3.1.) is available here as a single HTML file.

SRF has a dependancy on the ZTR package and the corresponding version of ZTR is 1.11.0. It is available here. ZTR provides an implementation of SRF in C.

A C++ implementation of SRF is available here.

The SRF project is accepting feature requests.