lra: A long read aligner for sequences and contigs

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

(2021) Haoyu Cheng et al.   NATURE METHODS

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   BIOINFORMATICS

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS