ISO/IEC 23092-2:2024

International
Standard
ISO/IEC 23092-2
Third edition
Information technology — Genomic
2024-03
information representation —
Part 2:
Coding of genomic information
Technologies de l'information — Représentation des informations
génomiques —
Partie 2: Codage des informations génomiques
Reference number
© ISO/IEC 2024
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© ISO/IEC 2024 – All rights reserved
ii
Contents Page
Foreword .vii
Introduction .viii
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Abbreviated terms . 6
5 Conventions . 6
5.1 General .6
5.2 Arithmetic operators .6
5.3 Logical operators .7
5.4 Relational operators .7
5.5 Bit-wise operators .7
5.6 Assignment operators .8
5.7 Range notation .8
5.8 Mathematical functions .8
5.9 Order of operation precedence .8
5.10 Variables, syntax elements and tables.9
5.11 Text description of logical operators .10
5.12 Processes .11
6 Syntax and semantics .12
6.1 Method of specifying syntax in tabular form . . 12
6.2 Bit ordering . 13
6.3 Specification of syntax functions and data types . 13
6.4 Semantics .14
7 Data structures . . 14
7.1 General .14
7.2 Data unit . 15
7.3 Raw reference .16
7.3.1 General .16
7.3.2 Syntax and semantics .16
7.4 Parameter set.16
7.4.1 Syntax and semantics .16
7.4.2 Encoding parameters .17
7.5 Access unit . 23
7.5.1 Syntax and semantics .24
7.5.2 Access unit types .27
8 Descriptors . .28
9 Sequencing reads . .31
9.1 General .31
9.2 Supported symbols .31
9.3 Paired-end reads . 33
9.4 Reverse-complement reads . 33
9.5 Data classes . 33
9.6 Aligned data . 34
9.7 Unaligned data . 35
10 Decoding process .35
10.1 General . 35
10.2 dataset_type = 0 or 1. 36
10.2.1 General . 36
10.2.2 References padding . 36
10.2.3 Type 1 AU (Class P) .37

© ISO/IEC 2024 – All rights reserved
iii
10.2.4 Type 2 AU (Class N) . 38
10.2.5 Type 3 AU (Class M) . 38
10.2.6 Type 4 AU (Class I) . 39
10.2.7 Type 5 AU (Class HM) .41
10.2.8 Type 6 AU (Class U) .41
10.3 dataset_type = 2 .42
10.3.1 General .42
10.3.2 Type 1 AU .43
10.3.3 Type 2 AU .43
10.3.4 Type 3 AU .43
10.3.5 Type 4 AU . 44
10.3.6 Type 6 AU . 44
10.4 Genomic descriptors . 44
10.4.1 General . 44
10.4.2 pos .45
10.4.3 rcomp .45
10.4.4 flags . 46
10.4.5 mmpos .47
10.4.6 mmtype. 49
10.4.7 clips . 53
10.4.8 ureads. 55
10.4.9 rlen . 56
10.4.10 pair .57
10.4.11 mscore . 64
10.4.12 mmap . 65
10.4.13 msar . 68
10.4.14 rtype . 69
10.4.15 rgroup .71
10.4.16 qv .71
10.4.17 rname . 75
10.4.18 rftp . 75
10.4.19 rftt .76
10.4.20 tokentype descriptors . 77
10.5 sequence . 85
10.5.1 General . 85
10.5.2 Aligned reads (Classes P, N, M, I, HM) . 85
10.5.3 Unmapped reads (Class HM, U) . 86
10.6 e-cigar . 86
10.6.1 Syntax . . 86
10.6.2 Decoding process for the first alignment . 88
10.6.3 Decoding process for other alignments . 95
10.6.4 Reference transformation . 95
11 Representation of reference sequences .96
11.1 External reference . 97
11.2 Embedded reference. 97
11.3 Computed reference . . 97
11.3.1 General . 97
11.3.2 Supported Algorithms . 97
11.3.3 Reference transformation . 98
11.3.4 PushIn . 98
11.3.5 Local assembly . 100
11.3.6 Global assembly . 101
12 Block payload parsing process .101
12.1 General . 101
12.2 Encoding Mode 0 . 102
12.3 Inverse binarizations . 103
12.3.1 General . 103
12.3.2 Binary (BI) . 103

© ISO/IEC 2024 – All rights reserved
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12.3.3 Truncated unary (TU) . 104
12.3.4 Exponential golomb (EG) . 104
12.3.5 Truncated exponential golomb (TEG) . 105
12.3.6 Signed truncated exponential golomb (STEG) . . 105
12.3.7 Split unit-wise truncated unary (SUTU) . 105
12.3.8 Signed split unit-wise truncated unary (SSUTU) . 106
12.3.9 Double truncated unary (DTU) . 106
12.3.10 Signed double truncated unary (SDTU) . 107
12.4 Decoder configuration . 107
12.4.1 Sequences and quality values . 107
12.4.2 Support values . 108
12.4.3 CABAC binarizations . . 109
12.4.4 Transformation parameters. 112
12.4.5 Msar descriptor and read identifiers . 113
12.4.6 State variables .114
12.5 Initialization process for context variables .117
12.6 Arithmetic decoding engine .117
12.6.1 Initialization .117
12.6.2 Arithmetic decoding process . 118
12.7 Decoding process for sequence descriptors . 124
12.7.1 General . 125
12.7.2 Block payload decoding process . 125
12.8 BSC decoding process . 139
12.8.1 decoding process . 139
13 Output format . .141
13.1 General .141
13.2 MPEG-G record .141
13.2.1 General .141
13.2.2 number_of_template_segments .143
13.2.3 number_of_record_segments .143
13.2.4 number_of_alignments .143
13.2.5 class_ID . 144
13.2.6 read_group_len . 144
13.2.7 reserved . 144
13.2.8 read_1_first . 144
13.2.9 seq_ID . 144
13.2.10 as_depth . 144
13.2.11 read_len . 144
13.2.12 qv_depth . 144
13.2.13 read_name_len . 144
13.2.14 read_name .145
13.2.15 read_group.145
13.2.16 sequence.145
13.2.17 quality_values .145
13.2.18 mapping_pos .145
13.2.19 ecigar_len .145
13.2.20 ecigar_string . . .145
13.2.21 reverse_comp .145
13.2.22 mapping_score .145
13.2.23 split_alignment .145
13.2.24 delta . 146
13.2.25 split_pos . 146
13.2.26 split_seq_ID . 146
13.2.27 flags . 146
13.2.28 more_alignments . 146
13.2.29 next_pos . 146
13.2.30 next_seq_ID . 146
13.3 Initialization process . 146

© ISO/IEC 2024 – All rights reserved
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Annex A (informative) Tokenization of reads identifiers .150
Annex B (informative) Mapping quality .152
Annex C (informative) Inverse binarization examples .153
Annex D  Block Sorting, Lossless Data Compression .157

© ISO/IEC 2024 – All rights reserved
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Foreword
ISO (the International Organization for Standardization) and IEC (the International Electrotechnical
Commission) form the specialized system for worldwide standardization. National bodies that are
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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 or www.iec.ch/members_experts/refdocs).
ISO and IEC draw attention to the possibility that the implementation of this document may involve the
use of (a) patent(s). ISO and IEC take no position concerning the evidence, validity or applicability of any
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received notice of (a) patent(s) which may be required to implement this document. However, implementers
are cautioned that this may not represent the latest information, which may be obtained from the patent
database available at www.iso.org/patents and https://patents.iec.ch. ISO and IEC shall not be held
responsible for identifying any or all such patent rights.
Any trade name used in this document is information given for the convenience of users and does not
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For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and expressions
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Organization (WTO) principles in the Technical Barriers to Trade (TBT) see www.iso.org/iso/foreword.html.
In the IEC, see www.iec.ch/understanding-standards.
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.
This third edition cancels and replaces the second edition (ISO/IEC 23092-2:2020), which has been
technically revised.
The main changes are as follows:
— inclusion of new low-complexity entropy coders in subclause 7.4.2.2 (Table 9): LZMA, ZSTD, BSC;
— inclusion of new indexed entropy coder in subclause 7.4.2.2 (Table 9): PROCRUSTES;
— inclusion of the specification of BSC decoding process in subclause 12.8 and Annex D;
— inclusion of a new flag (extended_alignment_info) in subclause 13.2.1 to represent split alignment
information in the compressed bitstream.
A list of all parts in the ISO/IEC 23092 series can be found on the ISO and IEC websites.
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 and
www.iec.ch/national-committees.

© ISO/IEC 2024 – All rights reserved
vii
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, the 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 sequencing read, or a paired sequencing 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.

© ISO/IEC 2024 – All rights reserved
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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 unit is too small 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 this
document. An access unit is composed of one block for each descriptor used to represent the information of
its genomic records; therefore, a block payload is the coded representation of all the data of the same type
(i.e. a descriptor) in a cluster.
In addition to clusters of genomic records comp
...