Pipeliner: software to evaluate the performance of bioinformatics pipelines for next-generation resequencing

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

(2014) Anthony Youzhi Cheng et al.   BIOINFORMATICS

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

(2014) B. Nevado et al.   MOLECULAR ECOLOGY

Quantifying single nucleotide variant detection sensitivity in exome sequencing

(2013) Alison M Meynert et al.   BMC BIOINFORMATICS

Characterizing Bias in Population Genetic Inferences from Low-Coverage Sequencing Data

(2013) Eunjung Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score

(2012) Hayan Lee et al.   BIOINFORMATICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

Neutrality Tests for Sequences with Missing Data

(2012) L. Ferretti et al.   GENETICS

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data

(2012) Jacob E. Crawford et al.   Frontiers in Genetics

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

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH