NCBI BLAST+ integrated into Galaxy

Wrangling Galaxy’s reference data

(2014) Daniel Blankenberg et al.   BIOINFORMATICS

Orione, a web-based framework for NGS analysis in microbiology

(2014) Gianmauro Cuccuru et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

(2014) Pratik D. Jagtap et al.   JOURNAL OF PROTEOME RESEARCH

Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in Streptomyces

(2014) Andreas Präg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dissemination of scientific software with Galaxy ToolShed

(2014) Daniel Blankenberg et al.   GENOME BIOLOGY

TALENoffer: genome-wide TALEN off-target prediction

(2013) Jan Grau et al.   BIOINFORMATICS

Web-based visual analysis for high-throughput genomics

(2013) Jeremy Goecks et al.   BMC GENOMICS

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

(2013) Mikel Egaña Aranguren et al.   Journal of Biomedical Semantics

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

(2013) Peter J.A. Cock et al.   PeerJ

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

Galaxy CloudMan: delivering cloud compute clusters

(2011) Enis Afgan et al.   BMC BIOINFORMATICS

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

Prokaryotic gene clusters: A rich toolbox for synthetic biology

(2010) Michael Fischbach et al.   Biotechnology Journal

myExperiment: a repository and social network for the sharing of bioinformatics workflows

(2010) Carole A. Goble et al.   NUCLEIC ACIDS RESEARCH

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS