Nature Genetics · 2018 · 56 citations · 54 references
Life SciencesGeneticsMolecular BiologyChromatin BiologyChromatin StructureEpigeneticsChromatinEpigenetic Regulation In DevelopmentNucleosome OrganizationNucleosome StructureRna InterferenceTranscriptional SilencingEpigenetic Gene SilencingEpigenetic Regulation Of Nuclear OrganizationEpigenetic SilencingMicrorna-induced Silencing ComplexNucleolar OrganizationTranscriptional Gene Silencing
54
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang, Tao Liu, Clifford A. Meyer et al. · Genome biology · 2008 · 19.9K citations · Full text