Introducing difference recurrence relations for faster semi-global alignment of long sequences

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

(2016) Jeff Daily   BMC BIOINFORMATICS

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

(2016) Benjamin Deonovic et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

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

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm

(2014) Joshua Loving et al.   BIOINFORMATICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

(2013) Mengyao Zhao et al.   PLoS One

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

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

A BIT-PARALLEL DYNAMIC PROGRAMMING ALGORITHM SUITABLE FOR DNA SEQUENCE ALIGNMENT

(2011) KOUICHI KIMURA et al.   Journal of Bioinformatics and Computational Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS