17.8k citations · 40.3k across the 19 of their papers we have counts for
20 papers
De novo reconstruction of satellite repeat units from sequence data
Yujie Zhang, Justin Chu, Haoyu Cheng +1
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble.…
Fast sequence to graph alignment using the graph wavefront algorithm
Haowen Zhang, Shiqi Wu, Srinivas Aluru +1
Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genome…
Metagenome assembly of high-fidelity long reads with hifiasm-meta
Xiaowen Feng, Haoyu Cheng, Daniel Portik +1
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome asse…
Robust haplotype-resolved assembly of diploid individuals without parental data
Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo +4
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction dat…
New strategies to improve minimap2 alignment accuracy
Heng Li
Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly…
Twelve years of SAMtools and BCFtools
Petr Danecek, James K. Bonfield, Jennifer Liddle +8
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago…
Haplotype-resolved de novo assembly with phased assembly graphs
Haoyu Cheng, Gregory T Concepcion, Xiaowen Feng +2
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into…
The design and construction of reference pangenome graphs
Heng Li, Xiaowen Feng, Chong Chu
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to m…
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems
Vasimuddin Md, Sanchit Misra, Heng Li +1
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds…
Identifying centromeric satellites with dna-brnn
Heng Li
Summary: Human alpha satellite and satellite 2/3 contribute to several percent of the human genome. However, identifying these sequences with traditional algorithms is computationa…
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
Motivation: Recent advances in sequencing technologies promise ultra-long reads of 100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genom…
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Heng Li
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome…
BGT: efficient and flexible genotype query across many samples
Heng Li
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to…
FermiKit: assembly-based variant calling for Illumina resequencing data
Heng Li
Summary: FermiKit is a variant calling pipeline for Illumina data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insert…
Correcting Illumina sequencing errors for human data
Heng Li
Summary: We present a new tool to correct sequencing errors in Illumina data produced from high-coverage whole-genome shotgun resequencing. It uses a non-greedy algorithm and shows…
Fast construction of FM-index for long sequence reads
Heng Li
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can buil…
Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples
Heng Li
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased wh…
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
Heng Li
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between l…
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
Heng Li
Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unit…
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Heng Li
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate geno…