ISO/IEC FDIS 23092-4

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.
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BEING ACCEPTABLE FOR INDUSTRIAL,
This document is circulated as received from the committee secretariat.
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Reference number
NATIONAL REGULATIONS.
ISO/IEC DIS 23092-4:2020(E)
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NOTIFICATION OF ANY RELEVANT PATENT
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PROVIDE SUPPORTING DOCUMENTATION. ISO/IEC 2020
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ISO/IEC DIS 23092-4:2020(E)
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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

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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

Any feedback or questions on this document should be directed to the user’s national standards body. A

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

— specifying an abstract representation of the sequencing data rather than a specific format with its

— 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

— 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

— allowing multiplexing of relevant meta-data information with the data since data and metadata are

— 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

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

— Speed and flexibility in the selective access to coded data, by means of newly designed data clustering

— Low latency in data transmission and consequent fast availability at remote locations, based on

— Built-in privacy and protection of sensitive information, thanks to a flexible framework which

— 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

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.

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

For these reasons, this document introduces the concept of access unit, which is the fundamental

The access unit is the smallest data structure that can be decoded by a decoder compliant with Part 2