The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

The SAMBA tool uses long reads to improve the contiguity of genome assemblies

(2022) Aleksey V. Zimin et al.   PLoS Computational Biology

Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references

(2022) Haiyi Lou et al.   Cell Systems

plotsr: visualizing structural similarities and rearrangements between multiple genomes

(2022) Manish Goel et al.   BIOINFORMATICS

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies

(2022) Alaina Shumate et al.   F1000Research

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

The structure, function and evolution of a complete human chromosome 8

(2021) Glennis A. Logsdon et al.   NATURE

A reference-quality, fully annotated genome from a Puerto Rican individual

(2021) Aleksey V Zimin et al.   GENETICS

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome

(2019) Zhenglin Du et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

(2018) Jung-Hyun Kim et al.   NUCLEIC ACIDS RESEARCH

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

The conservation landscape of the human ribosomal RNA gene repeats

(2018) Saumya Agrawal et al.   PLoS One

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

(2016) Jeff Daily   BMC BIOINFORMATICS

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

(2016) Kiana Mohajeri et al.   GENOME RESEARCH

Long-read sequencing and de novo assembly of a Chinese genome

(2016) Lingling Shi et al.   Nature Communications

Mechanisms of mRNA frame maintenance and its subversion during translation of the genetic code

(2015) Jack A. Dunkle et al.   BIOCHIMIE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The extent of genetic diversity of Epstein-Barr virus and its geographic and disease patterns: A need for reappraisal

(2009) Cindy M. Chang et al.   VIRUS RESEARCH

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE