Hello and many thanks for sharing your data.

I'm currently rebasecalling the data using the latest methods and noticed that many of the fast5 downloads are duplicates of other partitions. Are there reads missing and, if so, is it possible to obtain them please?

I've confirmed the duplication unpacking the files and comparing the reads. Its curious that the duplicate files have a different md5sum to the original; presumably the order in which the reads are packed in the file was not deterministic.

In all, I think there are the following equivalent partitions:

• 97, 98
• 145, 146, 147, 148
• 149, 150
• 151, 152
• 153, 154
• 155, 156, 157
• 164, 165, 166
• 167, 168
• 169, 170, 171
• 198, 199
• 200, 201
• 205, 206
• 209, 210
• 211, 212
• 219, 220

You can approximately confirm the duplication by looking at the file sizes provided by S3

aws s3 --no-sign-request ls --recursive  --summarize s3://nanopore-human-wgs/chm13/nanopore/fast5 | sort -gk 3 | cut -d ' ' -f 3,4 | rev |  uniq -c -f 1 | sort | rev

in your article ,the centromere was valiated by PFGE Southern blotting.I asked you Which company did this experiment in? we want to do this experiment for my project in the future,thanks~

Hey, it's really amazing that you made all this data available! I was just curious if you happened to have alignments (BAM or CRAM) to the latest v1.0 assembly?

I want to use my assembled genome to liftover reference genome, how to do it? thanks ~

dear author

I'd like to ask, when you assemble the centromere which data pool is applyed,I want to repeat this article

Hi, I am writing to ask whether you have some MySQL files available, just as files on the Ensembl? Thanks!

https://ftp.ensembl.org/pub/release-105/mysql/homo_sapiens_core_105_38/

Hi,
Is it possible to create a BSgenome package for CHM13 v1.0 and v1.1, which will make CHM13 accessible to many R packages?
Thanks.

The annotations available here: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v1.1.gene_annotation.v4.gff3.gz appear to be version 1.1 and do not contain Y chromosome data.

Is there a v2.0 GFF3 available with Y chromosome information?

Hello,

Do you have a bed file or coordinates for v1.0 assembly? I am filtering telomere enriched LR sequences mapped to v1.0. Thank you.

-Todd

Are there chain files somewhere to go from:
hg38 > chm13 1.1
chm13 1.1 > hg38
?

The only way I saw to achieve this was to go from hg38 > chm13 1.0 > chm13 1.1. It'd be preferred to just go directly to 1.1

Thanks!

I was looking at the gene annotation files, in particular, http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3
It looks like the file contains multiple problems, mostly touching exons with introns of size 0.
I can send examples

Hi, Has the CHM13 v1 reference undergone homopolymer compression? What is the recommended way to align PacBio Hifi reads to this reference? Are standard pbmm2 settings ok?

I've downloaded both the rel6 and rel7 fastq files. The rel6 fastq is 352GB in size while the rel7 fastq is only 100GB in size. Can I check if data is missing in the rel7 fastq files?

Hi, Are you aware of any CHM13 based imputation panels?

I have a few questions about these files

• Does the BNX file contain all the data necessary to create a truly complete Bionano optical genome mapping version of the CHM13 reference genome? Meaning will it contain telomere to telomere structural variant (SV) information (all the SVs in the genome from all the chromosomes)?
• Does the BNX file contain data from the Y chromosome as well?
• How was the cmap created? Was it created from the BNX file using bionano's software (bionano-solve or bionano access)? Can it be used as a reference for aligning other cmap files from samples processed using bionano's saphyr instrument?

Hi,

I just wanted to check if the sequencing_summary.txt file for the ONT reads is available for download somewhere?

Many thanks!

To whom it may concern,

I am hoping to use the CHM13 draft genome and the CCS reads to do some benchmarking of germline mutation calls. I was wondering which CCS reads were used for the draft v1.0 genome described in the post.

I found the following CCS reads in the SRA:

CHM13-CCS-20kb-m64062_190806_063919
CHM13-CCS-20kb-m64062_190803_042216
CHM13-CCS-15kb-m64062_190807_194840
CHM13-CCS-15kb-m64062_190804_172951
CHM13-CCS-11kb-m64015_190225_155953
CHM13-CCS-11kb-m64011_190228_190319
CHM13-CCS-11kb-m64015_190221_025712
CHM13-CCS-11kb-m64015_190224_013150

1. The X chromosome described in the paper Telomere-to-telomere assembly of a complete human X chromosome seems to be assembled from ONT ultra-long reads and 70X CLR reads
2. the draft genome described in the paper Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads is assembled from 11kb 24X sequence coveage CCS reads

I was not sure which HiFi reads were used for the draft v1.0 genome construction and I was wondering if someone could illuminate towards which HiFI reads that were not used in the assembly and the polishing process.

Best,
Sangjin

Hi Sergey,

Do you have fastqs for the ultra long data and the regular ont data as two separate datasets, or a way to figure that out from the rel3 fastq.gz?

I am trying to build length distributions for the different datasets.

Thanks!
Mitchell

Hi, Are you provide me a BED file of centromere locations and segmental duplication? I want to use this flie to analysis repeat sequence feature. Thank you so much !!

Hoping someone might be able to help in interpretation of a hg38 seg dup and how this sequence is represented in CHM13. We have two variants of interest at chr15:82229032 and chr15:82241415 (GRCh38) - both of which are within a known segmental duplication on chr15 (in GRCh38) https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1302038497_dN3q1vp2PMvkQkstUHwVIwAzCuA3&db=hg38&c=chr15&l=82130232&r=82262734&o=82190662&t=82270742&g=genomicSuperDups&i=chr15%3A84066812

We lifted these variants over using the hg38.t2t-chm13-v1.0.over.chain.gz chain to lift hg38 to CHM13 v1 and then the v1.0_to_v1.1.chain chain to lift CHM13 v1 to v1.1. Interestingly, with this approach, both coordinates lift over to the same position in CHM13v1.1 at chr15:80105532. One interpretation we considered was that the two seg dups in GRCh38 have been consolidated/collapsed into one in CHM13v1.1. Is that the correct interpretation? Could you confirm that chr15:80105532 (CHM13v1.1) is the correct liftover coordinate for both chr15:82229032 and chr15:82241415 (GRCh38) positions?

Additionally, when aligning our reads to CHM13v1.1 we don't see evidence for the chr15:82241415 (GRCh38) variant (at the same position, according to liftover). We interpreted this as the variant-supporting reads being (properly?) aligned to a different region of the CHM13v1.1 reference, instead of being (improperly?) aligned to the chr15:82241415 region where they supported a variant call. Would you say that's the correct interpretation?

Any insights here would be greatly appreciated! Thanks so much!

Can I ask which restriction enzyme is used for the Hi-C data in CHM13 cell line?

Is there any equivalent of an ENCODE blacklist available for the T2T reference genome?

Hello,
The fast5 for ONT data is so big.
Is there any access to all the ONT reads or the long ONT reads (99 Gbp of data in reads >50 kbp, 32x) in the format of "fasta.gz".
It would be much more convenient to download the data and usually doing assembly or SV detection will not need the quality information.

Thanks!

Hello,

Is there a table with the corresponding Ensembl IDs for the genes and transcripts in the CAT and Liftoff GFF3 version 2 annotation?

I want to use the T2T reference and annotation for an RNA-seq project, but for the purposes of this project it would be important to have the corresponding Ensembl IDs. I imagine others might have similar needs in the future.

Hi @skoren

Looks like the md5 hash for rel2.fastq.gz is written incorrectly. It is 35 characters in the README file. The first 3 characters seem to be a mistake (26s), the remainder is what I get when I calculate the hash (7e3f4ded02d500a3db0c76c84cdc42b9)

Hi,

are you aiming to integrate an existing (or newly assembled) Y chromosome at some point to make this a general purpose genome? Or is this not planned at present ?

I almost used this in a metagenomics reference sequence collection (i.e. for excluding non-microbial reads from the patient) but only just noticed that the Y chromosome was missing.

Thanks for your efforts.
Colin

I tried to extracted the cds sequences from the gff file.

gffread -g chm13.draft_v1.1.fasta -x cds.fa chm13.draft_v1.1.gene_annotation.v4.gff3

however, when trying to translate the cds to proteins, the open reading frame is not correct for quite many sequences. Is there a way to download the predicted protein sequences?

Hi,I am very happy to see your perfect aritcle had been preprinted,and we want to draw this coverage plot following your metnod ,that showing you in blow.can you tell me how to draw it or do you provide me code ? Thanks~

Is there a UCSC genome browser hub for CHM13-v1? That would make it easy to start doing easy liftovers, adding tracks, etc. Thanks.

Hello, please let me thank you first for this great effort and releasing publicly all data !
I was curious though concerning the PacBio HIFI raw data as I could not find the publishing directory of these.
Are only the CCS reads available or is there a possibility to access as well the raw sub-reads instead ?
Cheers

Good morning,
I would like to know how can i display the last assembly, including the gene annotations, in my laptop. Which programme do you use?
Thanks a lot.

Hi,
It would be super useful to activate both the View->In other genome, and the Liftover tools in the v1.0 and v1.1 UCSC browsers, both between them and to hg19/h38.

Many users will need very quick conversions of coordinates, without having to run the liftover command line tools with chain files.

Thanks.

Hi,

The bioRxiv paper says Canu was used for both data types (Nanopore and PacBio).

It seems that authors run Canu with combination of PB and ONT with the parameters (genomeSize=3.1g corMhapSensitivity=normal ovlMerThreshold=500 correctedErrorRate=0.085 trimReadsCoverage=2 trimReadsOverlap=500 -pacbio-raw)

Why didn't they run canu with multi platform parameter (-pacbio-raw -ont-raw)?

If I have a misunderstanding, please let me know.

Thanks a lot,
Changhan

Names of cell lines are confusing.

You say this data is generated from CH13TERT cell line, do you know if this is the same CHM13 from this paper (https://www.biorxiv.org/content/10.1101/635037v3.full) and the referenced assembly https://www.ncbi.nlm.nih.gov/assembly/GCA_002884485.1/??

How can I download the reference genome? I don't see any release or link,

Thanks,

Juber

Just a suggestion, feel free to ignore and close this issue but it might be helpful to provide the gzipped fasta files (e.g. chm13.draft_v1.0.fasta.gz) as bgzipped files. This will make it possible to use with bioinformatics tools requiring random access to the files.

Hello,

The GFF version 2.0 seems to be lacking mitochondrial encoded genes. Will you be releasing a new annotation including those?

Alternatively, would it be safe to assume that the coordinates for MT genes have not changed? If so I could copy them from the GRCh38 reference annotation in the meantime.

Thanks,
Bernardo

I'm having trouble using the provided GFF3 annotations from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v1.1.gene_annotation.v4.gff3.gz

Here's what I'm doing:
bcftools csq $VCF -f chm13.draft_v1.1.fasta -g chm13.draft_v1.1.gene_annotation.v4.gff3.gz -O z -o $VCF.csq.vcf.gz

And here's my ouput:

Parsing chm13.draft_v1.1.gene_annotation.v4.gff3.gz ...
ignored: chr1	CAT	gene	14253	21099	.	+	.	source_gene_common_name=AC114498.1;source_gene=ENSG00000235146.2;gene_biotype=lncRNA;gene_alternate_contigs=chr6:172104635-172111468;gene_id=CHM13_G0000001;gene_name=AC114498.1;transcript_modes=transMap;ID=CHM13_G0000001;Name=AC114498.1;source_transcript=N/A;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;paralogy=N/A;unfiltered_paralogy=N/A;alignment_id=N/A;frameshift=N/A;exon_anotation_support=N/A;intron_annotation_support=N/A;transcript_class=N/A;valid_start=N/A;valid_stop=N/A;proper_orf=N/A;extra_paralog=False
ignored: chr1	CAT	transcript	14253	21099	8940	+	.	source_transcript=ENST00000423796.1;source_transcript_name=AC114498.1-201;source_gene=ENSG00000235146.2;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=lncRNA;alignment_id=ENST00000423796.1-1;frameshift=nan;exon_annotation_support=1,1;intron_annotation_support=1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,basic;havana_gene=OTTHUMG00000002329.1;havana_transcript=OTTHUMT00000006707.1;paralogy=nan;unfiltered_paralogy=ENST00000423796.1-2;gene_alternate_contigs=chr6:172104635-172111468;source_gene_common_name=AC114498.1;transcript_id=CHM13_T0000001;gene_id=CHM13_G0000001;Parent=CHM13_G0000001;transcript_name=AC114498.1-201;ID=CHM13_T0000001;Name=AC114498.1;gene_name=CHM13_G0000001;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False
[csq.c:715 gff_id_parse] Could not parse the line, "Parent=transcript:" not present: chr1	CAT	exon	14253	14325	.	+	.	source_transcript=ENST00000423796.1;source_transcript_name=AC114498.1-201;source_gene=ENSG00000235146.2;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=lncRNA;alignment_id=ENST00000423796.1-1;exon_annotation_support=1,1;intron_annotation_support=1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,basic;havana_gene=OTTHUMG00000002329.1;havana_transcript=OTTHUMT00000006707.1;paralogy=nan;unfiltered_paralogy=ENST00000423796.1-2;gene_alternate_contigs=chr6:172104635-172111468;source_gene_common_name=AC114498.1;transcript_id=CHM13_T0000001;gene_id=CHM13_G0000001;Parent=CHM13_T0000001;transcript_name=AC114498.1-201;ID=exon:CHM13_T0000001:0;Name=AC114498.1;rna_support=N/A;reference_support=True;gene_name=CHM13_G0000001;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;frameshift=N/A;extra_paralog=False

Any guidance would be much appreciated! Thanks!

Is the 10X Chromium data available for download for CHM13?

Hello,

What is the recommended method to liftover hg38 panel targets bed to v1. 1? I see the chain file for v1. 0 to 1.1 but nothing for hg38. Look forward to trying!

Thanks

"You don't have access to this resource"... in Swedish ;)

https://sites.google.com/ucsc.edu/t2tworkinggroup/

Hello T2T team,

Congratulations on the finished genome - this is an absolutely staggering achievement!

Is there a link to the annotation used in the paper in GTF or GFF format? I've found the UCSC browser page, but the gene tracks there are very numerous and it's not clear how to download them.

Thank you in advance!

In your assembly summarization，only the 5 rDNA arrays remain unfinished. in future ,how to your team assembly those unfinished region ?

Hello,

Thanks for all your great work in building the CHM13 assembly! I would like to plot some of my results of v2.0 using karyoploteR, and I am able to build a custom ideogram, but I cannot find a file with the positions of the cytobands. I see the centromere and telomere files for v1.1 on the UCSC table browser, but I was wondering if there is a BED file with all of the cytoband positions?

Thanks,
Mike

Is there a chain file available to perform a life over from v1.1 to hg38?

Dear author,

I was wondering whether the T2T consortium could provide an over.chain file for liftOver of some coordinates from grch37/grch38 to CHM13 V1 draft genome and vice versa. I could create the file based on lastz alignments, but I thought having a publicly available would be useful for other as as well.

Regards,
Sangjin

Please put file sizes next to each file or an summary per section. This helps with planning storage requirements before downloading.

Hi,

I understand that the CHM13 nanopore datasets were generated at 4 different sites with PromethION sequencing done at UCD (runs 225 and 226), and MinION/GridION was presumably done at the other 3 sites (NHGRI, U of Nottingham, and UW).

From the T-to-T consortium paper (https://www.nature.com/articles/s41586-020-2547-7#Sec6), it was mentioned that "Most sequencing was performed on the Nanopore GridION with FLO-MIN106 or FLO-MIN106D R9 flow cells, with the exception of one Flongle flow cell used for testing."

Can I confirm if the GridION was used to generate the datasets from NHGRI, U of Nottingham, and UW? Alternatively, were some of the runs generated with a MinION? If so, is there a way for us to tell which runs these are?

Thanks for your help!

Hi, Are you able to upload a BED file of centromere locations? You have one for telomeres, but centromeres would also be useful. Thanks.

Hi, Do you have a BED file annotation of locations of segmental duplications for CHM13-v1? Thanks.