Heng Li

miniBUSCO improves genome assembly completeness evaluation by being faster and more accurate than BUSCO.

T1K is a computational method for accurately inferring KIR and HLA alleles from next-generation sequencing data, showing enrichment of KIR2DL4 in tumor-specific CD8+ T cells.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper identifies repeat-calling errors in nanopore sequencing of telomeres and shows that tuning basecalling models improves telomere analysis.

AGC provides a compact representation of assembled genomes, reducing storage space by 2-3 orders of magnitude while enabling efficient extraction of contig parts.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

CoLoRd compresses third-generation sequencing data by an order of magnitude without affecting downstream analysis accuracy.

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

CRISPAltRations is a cloud-based tool that improves the analysis of CRISPR-induced DNA repair events by outperforming existing software in annotating indels and HDR events.

The paper identifies more processed pseudogenes in humans and three great apes using long-read assemblies, showing higher discovery rates than previous short-read methods.

HTSlib provides a C library for efficient programmatic access to high-throughput sequencing data formats, with performance improvements and new features.

The paper introduces LISA, a machine learning-based index for accelerating sequence search in genomics, showing performance improvements over traditional indexes in various case studies.

bedtk is a toolkit for genomic interval manipulation that uses an implicit interval tree to enable fast overlap queries, outperforming existing tools in speed and memory usage.

This paper introduces a method for chromosome-scale haplotype-resolved genome assembly using long reads and long-range data, achieving high accuracy and contiguity in three human genomes.

The paper identifies extensive methylation changes in genes related to facial and vocal anatomy in modern humans compared to ancient humans and chimpanzees.

The paper introduces wtdbg2, a long-read assembler that is significantly faster than existing tools while maintaining comparable accuracy and contiguity for human genomes.

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.

The paper introduces a pedigree-graph-based method for haplotype-aware de novo assembly of related individuals using Illumina and PacBio data, achieving chromosomal-scale phased assemblies with low coverage.

The paper analyzes genetic variation in IGHV and TRBV immune receptor gene families across diverse human populations, finding distinct patterns of copy number and mutation.

The paper defines functional equivalence standards for genome sequencing pipelines to enable harmonized variant calling across diverse datasets with minimal batch effects.

The paper introduces a new synthetic-diploid benchmark for variant calling accuracy, derived from de novo PacBio assemblies of homozygous human cell lines to reduce bias in error rate estimation.

One mapper covers accurate short reads, noisy long reads, full-length cDNA and megabase contigs, running 3-4 times faster than short-read mappers at comparable accuracy.

This paper evaluates GRCh38 and de novo haploid assemblies, finding that GRCh38 remains superior for complex genomic regions and coding sequences despite improvements in newer assemblies.

This paper introduces genome graphs as an alternative to linear reference genomes, showing they improve read mapping and variant calling compared to the standard GRCh38 reference.

This study investigates the role of rare genetic variation in prostate cancer heritability using targeted sequencing of GWAS risk regions across multiple ancestries.

The paper updates the SAM/BAM format to support de novo assemblies by adding features like padded references and embedded sequences.

The paper tests if natural selection removed deleterious mutations less effectively in Europeans than West Africans, finding no significant difference.