ISO/IEC 23092-4:2020
(Main)Information technology — Genomic information representation — Part 4: Reference software
Information technology — Genomic information representation — Part 4: Reference software
This document specifies genomic information representation reference software, referred to as the genomic model (GM). This decoding software is provided to assess conformance to the requirements of ISO/IEC 23092-1 and ISO/IEC 23092-2.
Technologie de l'information — Représentation des informations génomiques — Partie 4: Logiciel de référence
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INTERNATIONAL ISO/IEC
STANDARD 23092-4
First edition
2020-10
Information technology — Genomic
information representation —
Part 4:
Reference software
Technologie de l'information — Représentation des informations
génomiques —
Partie 4: Logiciel de référence
Reference number
ISO/IEC 23092-4:2020(E)
©
ISO/IEC 2020
---------------------- Page: 1 ----------------------
ISO/IEC 23092-4:2020(E)
COPYRIGHT PROTECTED DOCUMENT
© ISO/IEC 2020
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting
on the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address
below or ISO’s member body in the country of the requester.
ISO copyright office
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii © ISO/IEC 2020 – All rights reserved
---------------------- Page: 2 ----------------------
ISO/IEC 23092-4:2020(E)
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Reference software modules . 1
4.1 General . 1
4.2 Copyright disclaimer for software modules . 2
5 Genomic model (GM). 2
5.1 GM availability . 2
5.2 Compilation and usage of the GM . 2
5.3 Decoding software . 3
5.3.1 Decoding software modules . 3
5.3.2 Feature availability. 3
© ISO/IEC 2020 – All rights reserved iii
---------------------- Page: 3 ----------------------
ISO/IEC 23092-4:2020(E)
Foreword
ISO (the International Organization for Standardization) and IEC (the International Electrotechnical
Commission) form the specialized system for worldwide standardization. National bodies that
are members of ISO or IEC participate in the development of International Standards through
technical committees established by the respective organization to deal with particular fields of
technical activity. ISO and IEC technical committees collaborate in fields of mutual interest. Other
international organizations, governmental and non-governmental, in liaison with ISO and IEC, also
take part in the work.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for
the different types of document should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www .iso .org/ directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject
of patent rights. ISO and IEC shall not be held responsible for identifying any or all such patent
rights. Details of any patent rights identified during the development of the document will be in the
Introduction and/or on the ISO list of patent declarations received (see www .iso .org/ patents) or the IEC
list of patent declarations received (see http:// patents .iec .ch).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO's adherence to the
World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT) see www .iso .org/
iso/ foreword .html.
This document was prepared by Joint Technical Committee ISO/IEC JTC 1, Information technology,
Subcommittee SC 29, Coding of audio, picture, multimedia and hypermedia information
A list of all parts in the ISO/IEC 23092 series can be found on the ISO website.
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www .iso .org/ members .html.
iv © ISO/IEC 2020 – All rights reserved
---------------------- Page: 4 ----------------------
ISO/IEC 23092-4:2020(E)
Introduction
The advent of high-throughput sequencing (HTS) technologies has the potential to boost the adoption
of genomic information in everyday practice, ranging from biological research to personalized genomic
medicine in clinics. As a consequence, an extraordinarily growing volume of generated data has
increased dramatically during the last few years, and an even more pronounced growth is expected in
the near future.
At the moment genomic information is mostly exchanged through a variety of data formats, such as
FASTA/FASTQ for unaligned sequencing reads and SAM/BAM/CRAM for aligned reads. With respect to
such formats, the ISO/IEC 23092 series provides a new solution for the representation and compression
of genome sequencing information by:
— Specifying an abstract representation of the sequencing data rather than a specific format with its
direct implementation.
— Being designed at a time point when technologies and use cases are more mature. This permits
addressing one limitation of the textual SAM format, for which the incremental ad-hoc addition of
features followed along the years, resulting in an overall redundant and suboptimal format which
was unnecessarily complicated.
— Separating free-field user-defined information with no clear semantics from the genomic data
representation. This allows a fully interoperable and automatic exchange of information between
different data producers.
— Allowing multiplexing of relevant metadata information with the data since data and metadata are
partitioned at different conceptual levels.
— Following a strict and supervised development process which has proven successful in the last
30 years in the domain of digital media for the transport format, the file format, the compressed
representation and the application program interfaces.
The ISO/IEC 23092 series provides the enabling technology that will allow the community to create an
ecosystem of novel, interoperable, solutions in the field of genomic information processing. In particular
it offers:
— Consistent, general and properly designed format definitions and data structures to store sequencing
and alignment information. A robust framework which can be used as a foundation to implement
different compression algorithms.
— Speed and flexibility in the selective access to coded data, by means of newly designed data clustering
and optimized storage methodologies.
— Low latency in data transmission and consequent fast availability at remote locations, based on
transmission protocols inspired by real-time application domains.
— Built-in privacy and protection of sensitive information, thanks to a flexible framework which
allows customizable secured access at all layers of the data hierarchy.
— Reliability of the technology and interoperability among tools and systems, owing to the provision
of a procedure to assess conformance to this document on an exhaustive dataset.
— Support to the implementation of a complete ecosystem of compliant devices and applications,
through the availability of a normative reference implementation covering the totality of the
ISO/IEC 23092 series.
The fundamental structure of the ISO/IEC 23092 series data representation is the genomic record. The
genomic record is a data structure consisting of either a single sequence read, or a paired sequence
read, and its associated sequencing and alignment information; it may contain detailed mapping and
alignment data, a single or paired read identifier (read name) and quality values.
© ISO/IEC 2020 – All rights reserved v
---------------------- Page: 5 ----------------------
ISO/IEC 23092-4:2020(E)
Without breaking traditional approaches, the genomic record introduced in the ISO/IEC 23092 series
provides a more compact, simpler and manageable data structure grouping all the information related
to a single DNA template, from simple sequencing data to sophisticated alignment information.
The genomic record, although it is an appropriate logic data structure for interaction and manipulation of
coded information, is not a suitable atomic data structure for compression. To achieve high compression
ratios, it is necessary to group genomic records into clusters and to transform the information of the
same type into sets of descriptors structured into homogeneous blocks. Furthermore, when dealing
with selective data access, the genomic record is
...
DRAFT INTERNATIONAL STANDARD
ISO/IEC DIS 23092-4
ISO/IEC JTC 1/SC 29 Secretariat: JISC
Voting begins on: Voting terminates on:
2020-01-22 2020-04-15
Information technology — Genomic information
representation —
Part 4:
Reference software
ICS: 35.040.99
THIS DOCUMENT IS A DRAFT CIRCULATED
FOR COMMENT AND APPROVAL. IT IS
THEREFORE SUBJECT TO CHANGE AND MAY
NOT BE REFERRED TO AS AN INTERNATIONAL
STANDARD UNTIL PUBLISHED AS SUCH.
IN ADDITION TO THEIR EVALUATION AS
BEING ACCEPTABLE FOR INDUSTRIAL,
This document is circulated as received from the committee secretariat.
TECHNOLOGICAL, COMMERCIAL AND
USER PURPOSES, DRAFT INTERNATIONAL
STANDARDS MAY ON OCCASION HAVE TO
BE CONSIDERED IN THE LIGHT OF THEIR
POTENTIAL TO BECOME STANDARDS TO
WHICH REFERENCE MAY BE MADE IN
Reference number
NATIONAL REGULATIONS.
ISO/IEC DIS 23092-4:2020(E)
RECIPIENTS OF THIS DRAFT ARE INVITED
TO SUBMIT, WITH THEIR COMMENTS,
NOTIFICATION OF ANY RELEVANT PATENT
RIGHTS OF WHICH THEY ARE AWARE AND TO
©
PROVIDE SUPPORTING DOCUMENTATION. ISO/IEC 2020
---------------------- Page: 1 ----------------------
ISO/IEC DIS 23092-4:2020(E)
COPYRIGHT PROTECTED DOCUMENT
© ISO/IEC 2020
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting
on the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address
below or ISO’s member body in the country of the requester.
ISO copyright office
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Fax: +41 22 749 09 47
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii © ISO/IEC 2020 – All rights reserved
---------------------- Page: 2 ----------------------
ISO/IEC DIS 23092-4:2020(E)
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 2
4 Abbreviated terms . 2
5 Copyright Disclaimer for Software Modules . 2
6 Genomic Model . 2
6.1 Genomic Model availability . 2
6.2 Compilation and usage of the Genomic Model . 3
6.3 Decoding Software . 3
6.3.1 Decoding Software modules . 3
6.3.2 Feature availability. 3
© ISO/IEC 2020 – All rights reserved iii
---------------------- Page: 3 ----------------------
ISO/IEC DIS 23092-4:2020(E)
Foreword
ISO (the International Organization for Standardization) and IEC (the International Electrotechnical
Commission) form the specialized system for worldwide standardization. National bodies that
are members of ISO or IEC participate in the development of International Standards through
technical committees established by the respective organization to deal with particular fields of
technical activity. ISO and IEC technical committees collaborate in fields of mutual interest. Other
international organizations, governmental and non-governmental, in liaison with ISO and IEC, also
take part in the work.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for
the different types of document should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www .iso .org/ directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject
of patent rights. ISO and IEC shall not be held responsible for identifying any or all such patent
rights. Details of any patent rights identified during the development of the document will be in the
Introduction and/or on the ISO list of patent declarations received (see www .iso .org/ patents) or the IEC
list of patent declarations received (see http:// patents .iec .ch).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO's adherence to the
World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT) see www .iso .org/
iso/ foreword .html.
This document was prepared by Joint Technical Committee ISO/IEC JTC 1, Information technology,
Subcommittee SC 29, Coding of audio, picture, multimedia and hypermedia information
A list of all parts in the ISO/IEC 23092 series can be found on the ISO website.
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www .iso .org/ members .html.
iv © ISO/IEC 2020 – All rights reserved
---------------------- Page: 4 ----------------------
ISO/IEC DIS 23092-4:2020(E)
Introduction
The advent of High-Throughput Sequencing (HTS) technologies has the potential to boost the adoption
of genomic information in everyday practice, ranging from biological research to personalized genomic
medicine in the clinic. As a consequence, an extraordinarily growing volume of generated data has been
recorded during the last few years, and an even more pronounced growth is expected in the near future.
At the moment genomic information is mostly exchanged through a variety of data formats, such as
FASTA/FASTQ for unaligned sequencing reads and SAM/BAM/CRAM for aligned reads. With respect
to such formats, ISO/IEC 23092 provides a new solution for the representation and compression of
genome sequencing information by:
— specifying an abstract representation of the sequencing data rather than a specific format with its
direct implementation
— being designed at a time point when technologies and use cases are more mature. This permits to
address one limitation of the textual SAM format, for which incremental ad-hoc addition of features
followed along the years, resulting in an overall redundant and suboptimal format which at the
same time results not general and unnecessarily complicated
— normatively separating free-field user-defined information with no clear semantics from the
normative genomic data representation. This allows a fully interoperable and automatic exchange
of information between different data producers.
— allowing multiplexing of relevant meta-data information with the data since data and metadata are
partitioned at different conceptual levels.
— following a strict and supervised development process which has proven successful in the last
30 years in the domain of digital media for the transport format, the file format, the compressed
representation and the application program interfaces.
This document provides the enabling technology that will allow the community to create an ecosystem
of novel, interoperable, solutions in the field of genomic information processing. In particular it offers:
— Consistent, general and properly designed format definitions and data structures to store sequencing
and alignment information. A robust framework which can be used as a foundation to implement
different compression algorithms
— Speed and flexibility in the selective access to coded data, by means of newly designed data clustering
and optimized storage methodologies
— Low latency in data transmission and consequent fast availability at remote locations, based on
transmission protocols inspired by real-time application domains
— Built-in privacy and protection of sensitive information, thanks to a flexible framework which
allows customizable secured access at all layers of the data hierarchy
— Reliability of the technology and interoperability among tools and systems, owing to the provision
of a normative procedure to assess conformance to the standard on an exhaustive dataset
— Support to the implementation of a complete ecosystem of compliant devices and applications,
through the availability of a normative reference implementation covering the totality of the
specification.
The fundamental structure of the ISO/IEC 23092 series data representation is the genomic record. The
genomic record is a data structure consisting of either a single sequence read, or a paired sequence
read, and its associated sequencing and alignment information; it may contain detailed mapping and
alignment data, a single or paired read identifier (read name) and quality values.
© ISO/IEC 2020 – All rights reserved v
---------------------- Page: 5 ----------------------
ISO/IEC DIS 23092-4:2020(E)
Without breaking traditional approaches, the genomic record introduced in the ISO/IEC 23092 series
provides a more compact, simpler and manageable data structure grouping all the information related
to a single DNA template, from simple sequencing data to sophisticated alignment information.
The genomic record, although it is an appropriate logic data structure for interaction and manipulation of
coded information, is not a suitable atomic data structure for compression. To achieve high compression
ratios, it is necessary to group genomic records into clusters and to transform the information of the
same type into sets of descriptors structured into homogeneous blocks. Furthermore, when dealing
with selective data access, the genomic record is a too small unit to allow effective and fast information
retrieval.
For these reasons, this document introduces the concept of access unit, which is the fundamental
structure for coding and access to information in the compressed domain.
The access unit is the smallest data structure that can be decoded by a decoder compliant with Part 2
of this Specification. An access unit is
...
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