MultiQC26 SAMtools23 fastp21 BWA18 Bowtie 212 Cutadapt10 FastQC10 Minimap210 BLAST9 BCFtools7 BEDTools7 MaBoSS7 PhysiCell7 SRA Software Toolkit7 lofreq6 MACS6 R5 snpEff5 Stacks5 antiSMASH4 Bandage4 BUSCO4 Cufflinks4 Galaxy4 kraken24 Racon4 Seurat4 shovill4 taxonomy_krona_chart4 TransDecoder4 Unicycler4 UniProt4 cisTEM3 GenomeScope 2.03 gffread3 Gromacs3 iVar3 MotionCor23 picard_samtofastq3 QualiMap3 QUAST3 RepeatMasker3 Scipion3 SPAdes3 STAR3 Vcflib3 AmberTools2 BRAKER12 Bwa-mem22 bx-python2 CellProfiler2 ChiRA2 DESeq22 Flye2 funannotate2 HISAT22 Infernal2 Medaka2 NanoPlot2 nanopolish2 NGSUtils2 Open Babel2 PredPrIn2 RDKit2 RepeatModeler2 seqtk2 SnpSift2 StringTie2 tophat22 Trimmomatic2 VADR2 vardict2 VarScan2 vcfanno2 vcfutils2 Variant Effect Predictor (VEP)2 VSEARCH2 XMIPP2 AdapterRemoval1 BBMap1 Bioconductor1 Biopython1 CARNIVAL1 cBioPortal1 ChemicalToolbox1 Clustal 1.8 (Clustal W, Clustal X)1 cuffdiff1 decoupleR1 EGA1 Filtlong1 FLASH1 FreeBayes1 GATK1 GEMINI1 HiFiAdapterFilt1 htseqcount1 iqtree1 MAPseq1 Merqury1 Meryl1 miniasm1 MOB-suite1 Metagenomic operational taxonomic units (mOTUs)1 nextstrain.org1 ngsReports1 OBITools1 PEAR1 pilon1 PLINK1 progeny1 Proteinortho1 protexcluder1 purge_dups1 SeqCode1 SeqSero21 SISTR1 Subread1 SuCOS1 Trim Galore1 More...

Galaxy197 Common Workflow Language62 Nextflow49 Python29 Jupyter26 Snakemake24 COMPSs18 Shell Script11 Workflow Description Language6 Bpipe5 KNIME5 Scipion5 R markdown3 Autosubmit1 Janis1 Perl1 Pi1 Rbbt1 Uniform Interface to Computing Resources1 More...

covid-1943 Bioinformatics24 Genomics22 Assembly21 Metagenomics21 Nextflow20 CWL16 workflow16 Alignment15 Galaxy15 SNPs15 Transcriptomics15 Annotation13 RNASEQ13 INDELs12 rna-seq12 variant_calling12 rna11 vgp11 GATK410 image processing10 variant calling10 Large-genome-assembly9 PyCOMPSs9 cancer8 Example8 imaging8 Machine Learning8 scRNAseq8 Supercomputer8 Tutorial8 Marenostrum IV7 Python7 scalable7 covid19.galaxyproject.org6 name:ERGA6 ONT6 PBS6 bpipe5 Climate5 groovy5 GTN5 illumina5 Metabolomics5 NCI5 pediatric5 Reviewed5 SARS-CoV-25 Virology5 ARTIC4 ChIP4 COMPSs4 copernicus4 FASTQ4 Gadi4 generic4 jupyter4 Laptop4 name:HiFi4 nanopore4 Proteomics4 rare diseases4 Retrosynthesis4 SAMTools4 VGP_curated4 WGS4 Workflows4 antimicrobial resistance3 binning3 BWA3 Classification3 cryoem3 Default-SDR3 DNA3 EOSC4Cancer3 FAIR workflows3 Germline3 HiFi3 identification3 Java3 kraken3 manta3 mapping3 MetaDEGalaxy3 mirna prediction3 name:ASSEMBLY+QC3 NCI-Gadi3 OME-Zarr3 Pathway Analysis3 pathway prediction3 protein3 S33 SANBI3 scipion3 scRNA-seq3 Snakemake3 spa3 STAR3 structural variants3 Virus3 16S2 Alternative splicing2 Amplicon2 bash2 bioimaging2 BROAD2 BWA-mem2 CellProfiler2 ChIP-seq2 CODEX22 collections2 Conversion2 cosifer2 DE_NOVO2 differential expression2 dislib2 DNA-seq2 Electron microscopy2 Epigenomics2 ExomeDepth2 exploration2 expression2 FastQC2 Flashlite2 gene set enrichment analysis2 genome2 GROMACS2 GWAS2 Hi-C2 hifiasm2 iwc2 kallisto2 linkage_map2 mass-spectrometry2 metabolic engineering2 metatranscriptomics2 molecular dynamics2 mpxv2 MS2 Multi-omics2 multi-specimen-input2 MultiQC2 name:DataQC2 name:HIC2 nf-core2 pathway design2 personalized medicine2 phylogenetics2 phylogenomics2 Pipeline2 QC2 Semantic Network Analysis2 shotgun2 Synthetic Biology2 Tophat22 TransBioNet2 trinity2 validated-2022-06-292 variant-analysis2 VARSCAN22 VCF2 WDL2 workflow4metabolomics2 10.3390/microorganisms100202921 10X1 18S1 ABR1 abricate1 air-quality1 alternative-splicing1 AMR1 AMR-detection1 annotsv1 astronomy1 ATACseq1 automated workflows1 BackTrackBB1 bacterial-genomics1 BAM1 BBduk1 bbmap1 Behavioral data1 benchmarking1 BGE1 BioBB1 Biodiversity1 bioformats1 bioformats2raw1 Biomedical Ontologies1 BioStudies1 blast1 Bootstrapping1 bowtie21 BQSR1 braken1 BUSCO1 carveme1 CATH1 causal inference1 Cellranger1 Cheminformatics1 CIRCexplorer21 circrna1 circRNA_finder1 CIRIquant1 cmip61 common data model1 community-detection1 Community_metrics1 comparative effectiveness1 Compomics1 container1 counts1 CUTnRUN1 Darwin core1 data annotation1 data fusion1 data integration1 Data package1 data retrieval and transformation1 data transformation1 data wrangling1 DataOne1 DCC1 DE1 de novo1 Deep learning1 DIAMOND1 differential_expression1 directed acyclic graph1 disease outcome prediction1 DL1 Domain-Domain interaction1 dRNAseq1 durg response simulation1 earth observation1 Earthquake Detection1 Ecological metadata language1 Ecology1 eDNA1 eFlows4HPC1 emergen_validated1 EML1 eml-annotation1 eosc-nordic1 ERGA1 EZyRB1 FAIR1 fastp1 featurecounts1 file conversion1 filtering1 find_circ1 Galaxy-E1 GATK1 GATK31 GC-MS1 GEM1 gene expression correlation1 gene expression data wrangling1 Gene ontology term sets similarity1 Gene Prioritization1 genetic design1 genome_assembly1 genomic ancestry1 geo database mining1 GLM1 global assemblies1 gnps1 Gravitational Waves1 GRIDS1 GRIDSS1 GUCFG2galaxy1 GUI1 HaplotyeCaller1 hCNV1 high-throughput1 high-throughput_sequencing_analysis1 hmdb1 host-pathogen PPIs1 HTSeq1 humann21 Hybrid Workflow1 image file format1 index1 international comparison1 isoform switching1 ITS1 Juicer1 Kratos Multiphysics1 LC-MS1 LiftOver1 Luigi & Rufus workflow1 MAG1 map1 MapSplice1 MARS-seq1 massbank1 MaxQuant1 memote1 Merqury1 Meryl1 Metabarcoding1 metagenome1 metaMS1 MGE1 microbial1 microscopy1 MIRACUM1 miRanda1 mlxv1 Mobilome1 model1 Modeling1 mpvx1 Multivariate1 Mutect21 name:ILLUMINA1 name:ONT1 name:PROFILING1 ncbi sra1 NCI Gadi1 ndvi1 networks1 NGFF1 NGS1 non-coding1 non-model1 Non-parametric1 nonspliced1 Nord 31 observation1 OME-TIFF1 openebench1 paired-end1 pangenome1 pangeo1 parallel1 pathogenicity score1 Pathway co-occurrence1 Perl1 Pfam1 polygenic risk score1 polygenic score1 pox1 prediction1 Presence_absence1 prokka1 Proline1 Protein domains1 protein interactin data triplification1 protein interactions database integration1 Protein-Protein interaction prediction1 proteins network augmentation1 public cancer datasets exploration1 purge_dups1 QTL mapping1 quality1 quantification1 Quast1 radio interferometry1 rdkit1 reads_selection1 reads_simulation1 Reconstruction1 Reduced Order Modeling1 referencegenome1 Regulatory Mendelian Mutation score1 RELIANCE1 ReMM1 Report1 rice1 RSeQC1 salmon1 sambamba1 scientific publication text mining1 Segemehl1 Segmentation1 Seismic Detection1 Semantic Comparison1 Semantic Interpretation1 sentinel-2 data1 sequence annotation1 sequence search1 SIM1 single particle analysis1 single-end1 singularity1 SKA1 smart-seq 21 smoove1 Somatic1 SPARK1 Species abundance1 spectra1 Statistics1 strandedness1 StringTie1 Supernova1 survivor1 SV1 SVD1 synthetic data1 TAD1 TargetScan1 tcga1 TELLSeq1 tiddit1 Tomography1 topologically associating domains1 Toxicology1 trajectories1 Trans-Proteomic1 transcriptome1 tumour1 Unicycler1 vaccines1 validaiton o protein interaction predictions1 variant1 variant pathogenicity prediction1 variation1 whole genome sequencing1 xcms1 More...

Genís Bayarri50 WorkflowHub Bot42 Bert Droesbeke16 Anna Syme16 Laura Rodriguez-Navas14 Sarah Williams14 Yvan Le Bras11 Raül Sirvent11 Ambarish Kumar10 Tracy Chew9 Cristóbal Gallardo9 Anne Fouilloux8 Bart Nijsse8 Jean-Marie Burel8 Douglas Lowe7 Miguel Vazquez7 Yasmmin Martins7 Diego De Panis6 Jasper Koehorst5 Johan Gustafsson5 Sergi Sayols5 Georgina Samaha5 Oliver Woolland5 Matthieu Muffato5 Melchior du Lac4 Martin Beracochea4 Willem de Koning4 johan Rollin4 Dennis Dollée4 Konstantinos Kyritsis4 Stian Soiland-Reyes3 Peter van Heusden3 Irene Sánchez3 Juma Bayjan3 Mike Thang3 Wolfgang Maier3 Anton Nekrutenko3 Jeanette Reinshagen3 Varsha Kale3 Pablo Riesgo Ferreiro3 Daniel Marchan3 Hervé Ménager2 Luca Pireddu2 Robin Long2 Beatriz Serrano-Solano2 Phil Ewels2 Pavankumar Videm2 Ross Thorne2 Sarah Beecroft2 Valentine Murigneux2 thodk2 Elida Schneltzer2 Pasi Korhonen2 Miguel Roncoroni2 Kary Ocaña2 Cristiane Taniguti2 Adam Tofilski2 Tina Tian2 Daan Hazelaar2 Andrea Furlani2 Tom Brown2 Fabrice Touzain2 francois moreews1 Camille Juigné1 Laura del Cano1 Ivan Topolsky1 ignacio eguinoa1 Andrea Giachetti1 Michael R. Crusoe1 Matteo Chiara1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 phytopat gembloux1 johan Rollin1 Marco De La Pierre1 Julian Uszkoreit1 Helena Rasche1 Qinqin Long1 Dennis Hendriksen1 Patrick Durand1 Cyril Noel1 Richard Lupat1 Javier Moldon1 Volodymyr Savchenko1 Johannes Köster1 Bianca Pasat1 Rob Edwards1 Valentin Tilloy1 Michael Roach1 Ryan Patterson-Cross1 Alexander Botzki1 Barry Digby1 panou@fleming.gr Panou1 Haris Zafeiropoulos1 Kaur Alasoo1 Hrishikesh Dhondge1 Marvin Martens1 Marlene Rezk1 Naga Kasinadhuni1 Casper de Visser1 Samuel Lambert1 Ekaterina Sakharova1 Alejandra Escobar1 Saskia Hiltemann1 bugra oezdemir1 Max Schubach1 Luc Cornet1 Felicita Gernhardt1 Nico Trummer1 Ang Guo1 Diego Garrido-Martín1 Roderic Guigó1 Bruno P. Kinoshita1 Luca Cozzuto1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Stevie Pederson1 Jeffrey Detras1 Thomas Gruber1 Marjan Meurisse1 Khaled Jum'ah1 Jorrit Mesman1 Elisabetta Spinazzola1 Cristian Tatu1 Rosa M Badia1 Anand Maurya1 Agata Kilar1 Vincent Hervé1 Jessica Gomez-Garrido1 Akshay Akshay1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Zafran Hussain Shah1 More...

BioBB Building Blocks60 iwc42 Australian BioCommons32 GalaxyProject SARS-CoV-221 Galaxy Australia21 QCIF Bioinformatics18 usegalaxy-eu14 Sydney Informatics Hub14 UNLOCK13 Workflows and Distributed Computing12 PNDB11 MGnify8 Galaxy Climate8 OME8 IBISBA Workflows7 Galaxy Training Network7 HoloFood at MGnify7 ERGA Assembly7 PerMedCoE7 yPublish - Bioinfo tools7 CWL workflow SARS-CoV-26 Integrated and Urban Plant Pathology Laboratory6 IMBforge5 UX trial team5 iPC: individualizedPaediatricCure5 Specimen Data Refinery5 Cluster Emergent del Cervell Humà5 NanoGalaxy4 Seq4AMR4 Biodata Analysis Group4 Tree of Life Genome Analysis4 nf-core3 SARS-CoV-2 Data Hubs3 EJPRD WP13 case-studies workflows3 CO2MICS Lab3 EU-Openscreen3 TRON gGmbH3 Euro-BioImaging3 SANBI Pathogen Bioinformatics3 Scipion CNB3 nf-core viralrecon2 V-Pipe2 EOSC-Life - Demonstrator 7: Rare Diseases2 Pawsey Supercomputing Research Centre2 SeBiMER2 Applied Computational Biology at IEG/HMGU2 INFRAFRONTIER workflows2 TransBioNet2 CRC Cohort2 Workflows Australia2 usegalaxy.be workflows2 Air Quality Prediction2 Read2Map2 ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression2 Apis-wings2 Workflows for geographic science2 Katdetectr2 ANSES-Ploufragan2 ERGA Annotation2 NMR Workflow1 COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource1 Italy-Covid-data-Portal1 EOSC-Life-WP6-Demos1 EOSC-Life WP31 Genomics Coordination Center1 Janis1 IAA-CSIC1 Snakemake-Workflows1 ODA1 FAME1 CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus1 HecatombDevelopment1 OpenEBench1 Bioinformatics and Biostatistics (BIO2 ) Core1 VIB Bioinformatics Core1 Single Cell Unit1 emo-bon1 CINECA1 Toxicology community1 Gyn Department1 Medizinisches Proteom-Center, Medical Bioinformatics1 AGRF BIO1 X-omics1 CAPSID1 KircherLab1 BCCM_ULC1 Computational Science at HZDR1 Big data in biomedicine1 TRE-FX1 Guigó lab1 Statistical genetics1 Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation1 Bioinformatics Unit @ CRG1 BSC-CES1 ELIXIR Proteomics1 Black Ochre Data Labs1 IRRI Bioinformatics Group1 Zavolan Lab1 Metabolomics-Reproducibility1 NGFF Tools1 Bioinformatics workflows for life science1 Helmholtz Scientific Project Workflow Platform1 BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection1 Lake Erken modelling setup1 EOSC-Life WP3 OC Team, cross RI project1 ARA-dev1 Mendel Centre for Plant Genomics and Proteomics1 Metagenomic tools1 Pillar I: Manufacturing1 eFlows4HPC general1 Polygenic Score Catalog1 MLme: Machine Learning Made Easy1 Dioscuri TDA1 MMV-Lab1 Tree of Life Genome Assembly1 Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data1 Bioinformatics Laboratory for Genomics and Biodiversity (LBGB)1 More...

Independent Teams202 BioExcel60 Australian BioCommons58 COVID-19 Biohackathon31 eFlows4HPC13 ERGA9 HoloFood7 DISSCo - Distributed System of Scientific Collections5 Sanger Tree of Life5 nf-core3 EOSC-Life3 ELIXIR Belgium2 EOSC-Life-WP61 BeYond-COVID (BY-COVID)1 JKU 1 IRRI-Bioinformatics1 HELIPORT1 Coupled Catchment Lake Modelling1 More...

Adam Hospital56 Genís Bayarri55 Anna Syme16 Bart Nijsse13 Jasper Koehorst12 Tracy Chew12 Yvan Le Bras10 Laura Rodriguez-Navas9 Rosemarie Sadsad9 Georgina Samaha8 Jean-Marie Burel8 Saskia Hiltemann7 Martin Beracochea6 Douglas Lowe6 José Mª Fernández6 Delphine Lariviere6 Diego De Panis6 Coline Royaux5 Sergi Sayols5 Javier Conejero5 Melchior du Lac4 Gareth Price4 Oliver Woolland4 Ambarish Kumar3 Juma Bayjan3 Friederike Ehrhart3 Ozan Ozisik3 Patrick Durand3 Laura Leroi3 Laurence Livermore3 Germán Royval3 Cristóbal Gallardo3 Cenna Doornbos3 Cali Willet3 Jeanette Reinshagen3 Konstantinos Kyritsis3 Jorge Ejarque3 Ivan Topolsky2 Luca Pireddu2 Anne Fouilloux2 Michael R. Crusoe2 Pavankumar Videm2 Valentine Murigneux2 Alexandre Cormier2 Cyril Noel2 Pierre Cuzin2 Mike Thang2 Philipp Gormanns2 Kary Ocaña2 Varsha Kale2 Ekaterina Sakharova2 Cristiane Taniguti2 Diego Garrido-Martín2 Roderic Guigó2 Andrea Furlani2 Stian Soiland-Reyes1 Camille Juigné1 Willem de Koning1 Pau Andrio1 Matthias Haimel1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 Sarah Beecroft1 Marco De La Pierre1 Julian Uszkoreit1 Richard Lupat1 Johannes Köster1 Valentin Tilloy1 Michael Roach1 Elida Schneltzer1 Luiz Gadelha1 Asier Gonzalez-Uriarte1 Wolfgang Maier1 Woosub Shin1 Ryan Patterson-Cross1 Barry Digby1 Haris Zafeiropoulos1 Hrishikesh Dhondge1 Kim Philipp Jablonski1 Pasi Korhonen1 Marvin Martens1 Tazro Inutano1 Marlene Rezk1 Casper de Visser1 Jasper Ouwerkerk1 Benjamin Wingfield1 Anna Niehues1 Marie-Dominique Devignes1 Samuel Lambert1 Alejandra Escobar1 Katherine Farquharson1 Lucas Cruz1 Pablo Riesgo Ferreiro1 Felicita Gernhardt1 Andrey Prjibelski1 Xiaokang Zhang1 Zavolan Lab1 Mahnoor Zulfiqar1 Stevie Pederson1 Veit Schwämmle1 Anton Korobeynikov1 Luiz Gadelha1 Vasiliki Panagi1 Jorrit Mesman1 Elisabetta Spinazzola1 Cristian Tatu1 Agata Kilar1 Jessica Gomez-Garrido1 Sagane Joye-Dind1 Akshay Akshay1 Phuong Doan1 Davide Gurnari1 David Yuan1 Justin Sonneck1 Zafran Hussain Shah1 More...

BioCommons ‘Bring Your Own Data’ Expansion Project39 Tutorials for BioExcel Building Blocks (BioBB)11 scRNAseq processing in galaxy8 IDR6 ERGA Assembly Galaxy HiFi & HiC Pipelines (Hifiasm-HiC + Purge_Dups + YaHS)6 16S Microbial Analysis with mothur (on Galaxy Australia)6 Freely accessible ready to use global infrastructure and workflows for SARS-CoV-2 monitoring5 BioExcel Building Blocks (BioBB) Protein MD Setup Tutorials5 HiFi genome assembly on Galaxy4 Vertebrate Genomes Pipelines (VGP) workflows3 CEITEC CryoEM Facility Workflows3 TronFlow2 Sanger Tree of Life Assembly method1 More...

Bioinformatics19 Sequence assembly16 Genetic variation15 Whole genome sequencing15 Population genomics9 Biodiversity8 Ecology8 Metagenomics8 Biomedical science7 Genomics7 Transcriptomics6 Gene transcripts4 Metagenomic sequencing4 Bioimaging3 Biological databases3 Compound libraries and screening3 Imaging3 Oncology3 Preclinical and clinical studies3 Protein interactions3 Sample collections3 Sequence analysis3 Sequencing3 Virology3 Data integration and warehousing2 Data mining2 Data quality management2 DNA mutation2 DNA polymorphism2 Drug discovery2 Exome sequencing2 Gene expression2 Gene structure2 Protein interaction experiment2 Quantitative genetics2 Rare diseases2 Workflows2 ChIP-seq1 Computer science1 Copy number variation1 Data submission, annotation and curation1 Data visualisation1 DNA packaging1 Environmental science1 Epigenomics1 Genetics1 Human genetics1 Machine learning1 Mapping1 Medical imaging1 Medical informatics1 Metabolomics1 Metatranscriptomics1 Microbiology1 Molecular interactions, pathways and networks1 Ontology and terminology1 Phylogenetics1 Protein folds and structural domains1 Proteomics1 Structural genomics1 Structural variation1 Taxonomy1 More...

Sequencing quality control13 Variant calling11 Sequence assembly7 Sequence clustering6 Variant filtering6 Genome assembly5 Sequence alignment5 De-novo assembly4 Data retrieval3 Haplotype mapping3 Sequence assembly validation3 Transcriptome assembly3 Annotation2 Conversion2 Gene-set enrichment analysis2 Genetic mapping2 Indel detection2 Modelling and simulation2 Prediction and recognition2 Protein interaction network analysis2 Protein interaction network prediction2 SNP annotation2 SNP detection2 Variant classification2 Antimicrobial resistance prediction1 Clustering1 Copy number variation detection1 Data handling1 Differential gene expression profiling1 Dimensionality reduction1 DNA barcoding1 Enrichment analysis1 Expression analysis1 Expression correlation analysis1 Format detection1 Gene expression profiling1 Genome analysis1 Genome comparison1 ID mapping1 Image analysis1 Mapping1 Metabolic pathway prediction1 Named-entity and concept recognition1 Phasing1 Protein-protein interaction analysis1 Relation extraction1 RNA-Seq analysis1 Scaffolding1 Sequence assembly visualisation1 Sequence contamination filtering1 Sequence cutting1 Sequence trimming1 Taxonomic classification1 Text annotation1 Text mining1 Transcription factor binding site prediction1 Validation1 Visualisation1 More...

Stable236 Work-in-progress72 Deprecated2

Passing31 All failing8 Not available1