The average number of T2T-CHM13 bases with two or with more than two alignments was about 32.4 Mb (around 1.0%) and about 20.0 Mb (around 0.6%), respectively. On average, per haploid assembly, these duplicated regions had about 82.20% and 39.82% overlap with the pericentomeric o...
Latest assembly release T2T-CHM13v2.0 (T2T-CHM13+Y) Complete T2T reconstruction of a human genome with Y. Changes from v1.1 is the addition of a finished chromosome Y from the GIAB HG002/NA24385 sample, sequenced both by GIAB and HPRC. This genome is also available at NCBI (GCA_0099147...
The average number of T2T-CHM13 bases with two or with more than two alignments was about 32.4 Mb (around 1.0%) and about 20.0 Mb (around 0.6%), respectively. On average, per haploid assembly, these duplicated regions had about 82.20% and 39.82% overlap with the pericentomeric o...
1d). Our assembly covered 96.54% (92.55–98.03%) of the GRCh38 reference and 93.59% (89.66–95.77%) of the T2T-CHM13 reference (Fig. 1d), showing that some of the genomic regions of our assemblies were systematically unassembled or could not be reliably aligned, probably owing to highly ...
(v0.16.1) as the reference genome. For the human datasets, we used the T2T assembly of CHM13 as the reference genome. The assemblies were further polished with NextPolish using short and long reads and these genomes were subsequently used to evaluate QV and gene completeness. Gene completeness...
align with the human genome. Then, we ran RepeatMasker to identify repeats in these contigs. We reported the number of unique sequences in each assembly as the number of base pairs that do not align to the pangenome, do not align to CHM13v2.0, and are not covered by RepeatMasker ...
{VERSION}-mc.seqfile printf "CHM13v2\thttps://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0_maskedY_rCRS.fa.gz\n" >> hprc-${VERSION}-mc.seqfile tail -n +2 Year1_assemblies_v2_genbank.index | awk '{print $1 ".1\t" $2}' | grep...
为了研究我们 58 个 CPC 样本的基因组组成,我们将 116 个组装体与 T2T-CHM13 对齐,并使用 Phased Assembly Variant caller17 (Methods) 检测每个样品的变体。我们观察到每个 CPC 样本平均有 11.22% (9.35-13.05%) 的小变异和 24.16% (19.72-29.3%) 的结构变异 (SV) 位于高度重复的区域(Extended Data Fig....
(CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without...
Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex