S-conLSH: alignment-free gapped mapping of noisy long reads

conLSH: Context based Locality Sensitive Hashing for mapping of noisy SMRT reads

(2020) Angana Chakraborty et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

(2018) Ehsan Haghshenas et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

(2016) Lars Hahn et al.   PLoS Computational Biology

Estimating evolutionary distances between genomic sequences from spaced-word matches

(2015) Burkhard Morgenstern et al.   Algorithms for Molecular Biology

rHAT: fast alignment of noisy long reads with regional hashing

(2015) Bo Liu et al.   BIOINFORMATICS

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Fast alignment-free sequence comparison using spaced-word frequencies

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono 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

SpEED: fast computation of sensitive spaced seeds

(2011) Lucian Ilie et al.   BIOINFORMATICS

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Near-optimal hashing algorithms for approximate nearest neighbor in high dimensions

(2008) Alexandr Andoni et al.   COMMUNICATIONS OF THE ACM