Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love, Wolfgang Huber, Simon Anders

Genome biology

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg

Nature Methods

Long-read SequencingSequence AssemblyNatural SciencesComputational BiologyMolecular Biology +5

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron M. Standley

Molecular Biology and Evolution

GeneticsMolecular BiologyMajor UpdateGenomicsSequence Alignment +15

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall

Bioinformatics

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

Aaron McKenna, Matthew G. Hanna, Eric Banks, +8

Genome Research

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

Yang Liao, Gordon K. Smyth, Wei Shi

Bioinformatics

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred Grabherr, Brian J. Haas, Moran Yassour, +17

Nature Biotechnology

Long-read SequencingFunctional GenomicsNatural SciencesGeneticsSequence Analysis +10

BLAST+: architecture and applications

Christiam Camacho, George Coulouris, Vahram Avagyan, +4

BMC Bioinformatics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, +2

Bioinformatics

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Bruce J. Walker, Thomas Abeel, Terrance Shea, +8

PLoS ONE

EngineeringGeneticsDiploid GenomesContiguous GenomesMolecular Biology +18