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Add T2T-CHM13v2.0 reference genome support (CHM13-T2T) #250

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aa9deeb
Add T2T-CHM13v2.0 reference genome support (CHM13-T2T)
ljwharbers Jun 11, 2026
87c3d22
Add CHM13-T2T transcript files to package
ljwharbers Jun 11, 2026
94ad652
Fix CHM13-T2T chrY TSB checksum for unmasked iGenomes reference
ljwharbers Jun 12, 2026
1c000aa
Add CHM13-T2T to supported genomes list in README intro
ljwharbers Jun 19, 2026
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

## [Unreleased]

### Added
- Added support for the T2T-CHM13v2.0 human reference genome (CHM13-T2T), nuclear chromosomes only (1–22, X, Y), WGS matrices, distributed via the AlexandrovLab FTP.

## [1.3.6] - 2025-10-28

### Added
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7 changes: 5 additions & 2 deletions README.md
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Expand Up @@ -29,7 +29,7 @@ The framework is written in PYTHON, however, it also requires the following soft
* WGET version 1.9 or RSYNC if you have a firewall

By default the installation process will save the FASTA files for all chromosomes for the default genome
assemblies (GRCh37, GRCH38, mm10, mm9, rn6). As a result, ~3 Gb of storage must be available for the downloads for each genome.
assemblies (CHM13-T2T, GRCh37, GRCh38, mm10, mm9, rn6). As a result, ~3 Gb of storage must be available for the downloads for each genome.

**QUICK START GUIDE**

Expand Down Expand Up @@ -83,7 +83,7 @@ View the table below for the full list of parameters.
| ------ | ----------- | ----------- | ----------- |
| Required | | | |
| | project | String | The name of the project. |
| | reference_genome | String | The name of the reference genome. Full list of genomes under **Supported Genomes** section. Supported values include the following: {c_elegans, dog, ebv, GRCh37, GRCh38, mm9, mm10, mm39, rn6, yeast} |
| | reference_genome | String | The name of the reference genome. Full list of genomes under **Supported Genomes** section. Supported values include the following: {c_elegans, CHM13-T2T, dog, ebv, GRCh37, GRCh38, mm9, mm10, mm39, rn6, yeast} |
| | path_to_input_files | String | The path to the input files. |
| Optional | | | |
| | exome | Boolean | Downsamples mutational matrices to the exome regions of the genome. Default value False. |
Expand Down Expand Up @@ -204,6 +204,9 @@ SigProfilerMatrixGenerator cnv_matrix_generator BATTENBERG ./SigProfilerMatrixGe

This tool currently supports the following genomes:

T2T-CHM13v2.0 [CHM13-T2T] (Telomere-to-Telomere Consortium CHM13 assembly v2.0), INSDC
Assembly GCA_009914755.4. Nuclear chromosomes only (1–22, X, Y; no mitochondrion). WGS matrices supported.

GRCh38.p12 [GRCh38] (Genome Reference Consortium Human Reference 38), INSDC
Assembly GCA_000001405.27, Dec 2013. Released July 2014. Last updated January 2018. This genome was downloaded from ENSEMBL database version 93.38.

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4 changes: 2 additions & 2 deletions SigProfilerMatrixGenerator/controllers/cli_controller.py
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Expand Up @@ -53,7 +53,7 @@ def parse_arguments_install(args: List[str]) -> argparse.Namespace:
parser = argparse.ArgumentParser(description="Install reference genome files.")
parser.add_argument(
"genome",
help="The reference genome to install. Supported genomes include {c_elegans, dog, ebv, GRCh37, GRCh38, mm9, mm10, mm39, rn6, rn7, yeast}.",
help="The reference genome to install. Supported genomes include {c_elegans, CHM13-T2T, dog, ebv, GRCh37, GRCh38, mm9, mm10, mm39, rn6, rn7, yeast}.",
)
parser.add_argument(
"-l",
Expand Down Expand Up @@ -85,7 +85,7 @@ def parse_arguments_matrix_generator(args: List[str]) -> argparse.Namespace:
parser.add_argument("project", help="The name of the project.")
parser.add_argument(
"reference_genome",
help="The name of the reference genome. Supported values {c_elegans, dog, ebv, GRCh37, GRCh38, mm9, mm10, mm39, rn6, rn7, yeast}.",
help="The name of the reference genome. Supported values {c_elegans, CHM13-T2T, dog, ebv, GRCh37, GRCh38, mm9, mm10, mm39, rn6, rn7, yeast}.",
)
parser.add_argument("path_to_input_files", help="The path to the input files.")

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8,274 changes: 8,274 additions & 0 deletions SigProfilerMatrixGenerator/references/chromosomes/transcripts/CHM13-T2T/10_transcripts.txt
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2 changes: 1 addition & 1 deletion SigProfilerMatrixGenerator/scripts/MutationMatrixGenerator.py
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Expand Up @@ -223,7 +223,7 @@ def BED_sorting(bed_file_path, genome):
],
**{
g: common_chrom_list
for g in ["GRCh37", "GRCh38", "dog", "ebv", "mm10", "mm9", "mm39", "rn6"]
for g in ["GRCh37", "GRCh38", "CHM13-T2T", "dog", "ebv", "mm10", "mm9", "mm39", "rn6"]
},
}

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9 changes: 9 additions & 0 deletions SigProfilerMatrixGenerator/scripts/SigProfilerMatrixGeneratorFunc.py
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Expand Up @@ -1597,6 +1597,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -1729,6 +1730,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -1880,6 +1882,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -2013,6 +2016,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -2240,6 +2244,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -2370,6 +2375,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -2502,6 +2508,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -2637,6 +2644,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down Expand Up @@ -2768,6 +2776,7 @@ def SigProfilerMatrixGeneratorFunc(
for genome in [
"GRCh37",
"GRCh38",
"CHM13-T2T",
"dog",
"ebv",
"mm10",
Expand Down
26 changes: 26 additions & 0 deletions SigProfilerMatrixGenerator/scripts/reference_genome_manager.py
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Expand Up @@ -102,6 +102,32 @@
"X": "d5edbea3cf5d1716765dd4a7b41b7656",
"MT": "dfd6db5743d399516d5c8dadee5bee78",
},
"CHM13-T2T": {
"1": "8160d885ea68cbd9e1a85f1a62f5c0f1",
"2": "5041bd8918b488102bd3fc17f4eff66e",
"3": "b499fea5aea8934cb8de2531157d49ec",
"4": "a2a3a52de2cca0e9fb5781901e1dfba8",
"5": "ee7f9612de6e8b1ec484c02b2b31e9fe",
"6": "2f9202597543ae1adc1dd31571a9c3d2",
"7": "be89f4bcc4553389fcc4e5f225db77da",
"8": "b0934433605dca7314235cc4059de0bb",
"9": "c669a1e483304201a6afa38ea0cedc53",
"10": "272a6ea1ec1bbbc3d5f34bd59df76457",
"11": "7bfa1f75f0c08c7ae7ff660f3171c6a6",
"12": "5fb792acd7f9cb00b1cc707b28d13723",
"13": "40cc90706b67aca49d409ef158e00685",
"14": "1a10df3d0fb9206d93fc3791666a54ae",
"15": "c60b41404acf203ffff4251c95ccb94c",
"16": "130a73687af01742dd35b0b5fbc225bb",
"17": "3b0ad5efe98372b5bf3e18d5938098de",
"18": "df7f62810c54fa7aa2d0c20481344252",
"19": "1e9f2c8bb1f11e45c1789a3e69c03094",
"20": "548df0167cbd6401d5f5b1c1050f7065",
"21": "460c01106a2402a25591a625c6a8ff73",
"22": "8d3aa47b4456add9d0b78cb70b155fda",
"X": "13dea22db0695374c214c15211c65424",
"Y": "3a5cc4f01eaa1eef9a34f9d5bd09ca3b",
},
"GRCh38_havana": {
"1": "c4ef4ee14a4f0f7b319e9ed01f2a9742",
"2": "189cb33da673afcf161b7724d78d314b",
Expand Down