AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

Genome-wide discovery of human splicing branchpoints

(2015) Tim R. Mercer et al.   GENOME RESEARCH

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

(2015) Michael B Clark et al.   NATURE METHODS

BatAlign: an incremental method for accurate alignment of sequencing reads

(2015) Jing-Quan Lim et al.   NUCLEIC ACIDS RESEARCH

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data

(2014) Swetansu Pattnaik et al.   BMC BIOINFORMATICS

Performance comparison of four exome capture systems for deep sequencing

(2014) Chandra Sekhar Chilamakuri et al.   BMC GENOMICS

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

(2014) Faraz Hach et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

YOABS: yet other aligner of biological sequences—an efficient linearly scaling nucleotide aligner

(2012) V. L. Galinsky   BIOINFORMATICS

SRmapper: a fast and sensitive genome-hashing alignment tool

(2012) Paul M. Gontarz et al.   BIOINFORMATICS

Fast and accurate read alignment for resequencing

(2012) John C. Mu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH