Workflows

MultiQC24 SAMtools23 fastp18 BWA14 Bowtie 211 Cutadapt10 Minimap29 FastQC8 BEDTools7 SRA Software Toolkit7 BLAST6 lofreq6 BCFtools5 MACS5 snpEff5 Stacks5 antiSMASH4 Bandage4 Cufflinks4 kraken24 Racon4 shovill4 taxonomy_krona_chart4 TransDecoder4 Unicycler4 UniProt4 BUSCO3 GenomeScope 2.03 gffread3 Gromacs3 iVar3 picard_samtofastq3 QualiMap3 QUAST3 Vcflib3 AmberTools2 Bwa-mem22 bx-python2 CellProfiler2 ChiRA2 DESeq22 Flye2 Medaka2 NanoPlot2 nanopolish2 NGSUtils2 Open Babel2 RDKit2 SPAdes2 STAR2 tophat22 Trimmomatic2 VSEARCH2 BBMap1 ChemicalToolbox1 Clustal 1.8 (Clustal W, Clustal X)1 cuffdiff1 EGA1 Filtlong1 FLASH1 FreeBayes1 funannotate1 GEMINI1 HiFiAdapterFilt1 HISAT21 htseqcount1 iqtree1 Merqury1 miniasm1 MOB-suite1 nextstrain.org1 PEAR1 pilon1 Proteinortho1 purge_dups1 RepeatMasker1 SeqCode1 SISTR1 StringTie1 Subread1 SuCOS1 Trim Galore1 VarScan1 More...

Galaxy132 Common Workflow Language51 Nextflow31 Jupyter18 Python16 Snakemake14 Shell Script11 Bpipe5 KNIME5 Workflow Description Language5 PyCOMPSs3 Scipion2 Janis1 R markdown1 More...

covid-1942 Assembly21 Alignment15 Nextflow15 SNPs14 Genomics13 INDELs13 CWL12 Galaxy12 workflow12 RNASEQ11 rna-seq10 variant_calling10 GATK49 Large-genome-assembly9 Metagenomics9 rna9 Transcriptomics9 Annotation8 cancer8 ONT7 scalable7 covid19.galaxyproject.org6 PBS6 vgp6 Bioinformatics5 bpipe5 Climate5 groovy5 illumina5 NCI5 pediatric5 Virology5 copernicus4 FASTQ4 Gadi4 generic4 rare diseases4 Retrosynthesis4 SAMTools4 variant calling4 WGS4 ARTIC3 BWA3 ChIP3 Classification3 Default-SDR3 DNA3 HiFi3 image processing3 kraken3 manta3 MetaDEGalaxy3 mirna prediction3 nanopore3 NCI-Gadi3 Pathway Analysis3 pathway prediction3 protein3 Proteomics3 scRNA-seq3 STAR3 structural variants3 16S2 Amplicon2 binning2 BROAD2 CellProfiler2 CODEX22 collections2 COMPSs2 cosifer2 differential expression2 DNA-seq2 ExomeDepth2 exploration2 FAIR workflows2 FastQC2 Flashlite2 genome2 GROMACS2 GTN2 Hi-C2 hifiasm2 identification2 iwc2 jupyter2 kallisto2 linkage_map2 mapping2 metabolic engineering2 Metabolomics2 molecular dynamics2 mpxv2 multi-specimen-input2 MultiQC2 nf-core2 pathway design2 phylogenetics2 phylogenomics2 PyCOMPSs2 QC2 Semantic Network Analysis2 Snakemake2 Synthetic Biology2 Tophat22 TransBioNet2 trinity2 validated-2022-06-292 VARSCAN22 VCF2 WDL2 10X1 18S1 ABR1 abricate1 air-quality1 Alternative splicing1 annotsv1 antimicrobial resistance1 astronomy1 ATACseq1 BackTrackBB1 bacterial-genomics1 BAM1 bash1 BBduk1 bbmap1 Behavioral data1 benchmarking1 BioBB1 Biodiversity1 bioimaging1 Biomedical Ontologies1 blast1 Bootstrapping1 bowtie21 BQSR1 braken1 BUSCO1 BWA-mem1 carveme1 CATH1 Cellranger1 ChIP-seq1 CIRCexplorer21 circrna1 circRNA_finder1 CIRIquant1 cmip61 community-detection1 Community_metrics1 Consensus1 container1 Conversion1 counts1 CUTnRUN1 Darwin core1 data integration1 Data package1 DataOne1 DCC1 DE1 de novo1 DE_NOVO1 DIAMOND1 differential_expression1 DL1 dRNAseq1 earth observation1 Earthquake Detection1 Ecological metadata language1 Ecology1 eDNA1 Electron microscopy1 emergen_validated1 EML1 eml-annotation1 eosc-nordic1 Epigenomics1 expression1 FAIR1 fastp1 featurecounts1 filtering1 find_circ1 Galaxy-E1 GATK1 GATK31 GEM1 Gene Prioritization1 genetic design1 genome_assembly1 Germline1 GLM1 global assemblies1 Gravitational Waves1 GRIDS1 GRIDSS1 GWAS1 HaplotyeCaller1 HTSeq1 humann21 imaging1 index1 ITS1 Juicer1 LiftOver1 Machine Learning1 map1 MapSplice1 MARS-seq1 mass-spectrometry1 memote1 Merqury1 Meryl1 Metabarcoding1 metagenome1 metatranscriptomics1 microbial1 miRanda1 mlxv1 model1 Modeling1 mpvx1 Multi-omics1 Multivariate1 Mutect21 name:ONT1 NCI Gadi1 ndvi1 networks1 non-coding1 non-model1 Non-parametric1 nonspliced1 observation1 openebench1 pangenome1 pangeo1 parallel1 pathogenicity score1 Pfam1 Pipeline1 pox1 Presence_absence1 prokka1 Protein domains1 purge_dups1 QTL mapping1 quality1 quantification1 Quast1 radio interferometry1 reads_selection1 reads_simulation1 Reconstruction1 referencegenome1 Regulatory Mendelian Mutation score1 RELIANCE1 ReMM1 Report1 RSeQC1 salmon1 sambamba1 SARS-CoV-21 Segemehl1 Segmentation1 Seismic Detection1 Semantic Comparison1 Semantic Interpretation1 sentinel-2 data1 shotgun1 single particle analysis1 singularity1 SKA1 smart-seq 21 smoove1 Somatic1 SPARK1 Species abundance1 Statistics1 strandedness1 StringTie1 Supernova1 survivor1 SV1 TAD1 TargetScan1 tcga1 TELLSeq1 tiddit1 Tomography1 topologically associating domains1 Toxicology1 trajectories1 transcriptome1 tumour1 Unicycler1 variant pathogenicity prediction1 variant-analysis1 variation1 Virus1 whole genome sequencing1 Workflows1 More...

Genís Bayarri38 WorkflowHub Bot24 Bert Droesbeke16 Anna Syme16 Laura Rodriguez-Navas13 Ambarish Kumar10 Tracy Chew9 Anne Fouilloux8 Bart Nijsse8 Douglas Lowe6 Cristóbal Gallardo6 Jasper Koehorst5 Sergi Sayols5 Oliver Woolland5 Melchior du Lac4 Willem de Koning4 Johan Gustafsson4 johan Rollin4 Georgina Samaha4 Martin Beracochea3 Yvan Le Bras3 Irene Sánchez3 Juma Bayjan3 Jean-Marie Burel3 Mike Thang3 Anton Nekrutenko3 Jeanette Reinshagen3 Pablo Riesgo Ferreiro3 Stian Soiland-Reyes2 Hervé Ménager2 Luca Pireddu2 Robin Long2 Beatriz Serrano-Solano2 Phil Ewels2 Pavankumar Videm2 Ross Thorne2 Sarah Beecroft2 thodk2 Elida Schneltzer2 Pasi Korhonen2 Miguel Roncoroni2 Kary Ocaña2 Raül Sirvent2 Cristiane Taniguti2 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 Valentine Murigneux1 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 Dennis Dollée1 Saskia Hiltemann1 Adam Tofilski1 Max Schubach1 Luc Cornet1 Felicita Gernhardt1 Nico Trummer1 Ang Guo1 Diego Garrido-Martín1 Roderic Guigó1 Luca Cozzuto1 More...

BioBB Building Blocks48 Australian BioCommons29 iwc24 GalaxyProject SARS-CoV-221 Galaxy Australia21 UNLOCK13 Sydney Informatics Hub13 usegalaxy-eu11 Galaxy Climate8 IBISBA Workflows7 CWL workflow SARS-CoV-26 Integrated and Urban Plant Pathology Laboratory6 MGnify5 IMBforge5 UX trial team5 iPC: individualizedPaediatricCure5 Specimen Data Refinery5 NanoGalaxy4 Galaxy Training Network3 nf-core3 PNDB3 EJPRD WP13 case-studies workflows3 QCIF Bioinformatics3 CO2MICS Lab3 OME3 EU-Openscreen3 TRON gGmbH3 nf-core viralrecon2 V-Pipe2 SARS-CoV-2 Data Hubs2 EOSC-Life - Demonstrator 7: Rare Diseases2 Pawsey Supercomputing Research Centre2 SeBiMER2 Applied Computational Biology at IEG/HMGU2 TransBioNet2 CRC Cohort2 Workflows Australia2 usegalaxy.be workflows2 Cluster Emergent del Cervell Humà2 Read2Map2 ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression2 NMR Workflow1 COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource1 Italy-Covid-data-Portal1 EOSC-Life-WP6-Demos1 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 Air Quality Prediction1 CAPSID1 Seq4AMR1 KircherLab1 Apis-wings1 BCCM_ULC1 Computational Science at HZDR1 Big data in biomedicine1 Guigó lab1 Statistical genetics1 Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation1 Bioinformatics Unit @ CRG1 More...

Independent Teams132 BioExcel48 Australian BioCommons41 COVID-19 Biohackathon31 DISSCo - Distributed System of Scientific Collections5 nf-core3 EOSC-Life2 ELIXIR Belgium2 EOSC-Life-WP61 JKU 1 More...

Adam Hospital44 Genís Bayarri43 Anna Syme16 Bart Nijsse13 Jasper Koehorst12 Tracy Chew11 Laura Rodriguez-Navas9 Rosemarie Sadsad9 Georgina Samaha7 José Mª Fernández6 Delphine Lariviere6 Douglas Lowe5 Sergi Sayols5 Melchior du Lac4 Martin Beracochea4 Gareth Price4 Oliver Woolland4 Ambarish Kumar3 Juma Bayjan3 Friederike Ehrhart3 Ozan Ozisik3 Jean-Marie Burel3 Patrick Durand3 Laura Leroi3 Laurence Livermore3 Germán Royval3 Cenna Doornbos3 Cali Willet3 Jeanette Reinshagen3 Ivan Topolsky2 Luca Pireddu2 Anne Fouilloux2 Pavankumar Videm2 Alexandre Cormier2 Cyril Noel2 Pierre Cuzin2 Kary Ocaña2 Cristiane Taniguti2 Diego Garrido-Martín2 Roderic Guigó2 Stian Soiland-Reyes1 Camille Juigné1 Willem de Koning1 Yvan Le Bras1 Coline Royaux1 Pau Andrio1 Michael R. Crusoe1 Matthias Haimel1 Carlos Oscar Sorzano Sanchez1 Paul Brack1 Sarah Beecroft1 Marco De La Pierre1 Julian Uszkoreit1 Valentine Murigneux1 Richard Lupat1 Mike Thang1 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 Anna Niehues1 Marie-Dominique Devignes1 Varsha Kale1 Ekaterina Sakharova1 Katherine Farquharson1 Saskia Hiltemann1 Lucas Cruz1 Pablo Riesgo Ferreiro1 Felicita Gernhardt1 More...

BioCommons ‘Bring Your Own Data’ Expansion Project39 Tutorials for BioExcel Building Blocks (BioBB)11 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 IDR3 Vertebrate Genomes Pipelines (VGP) workflows3 TronFlow2 More...

Sequence assembly16 Genetic variation9 Population genomics9 Whole genome sequencing9 Metagenomics6 Bioinformatics5 Metagenomic sequencing4 Transcriptomics4 Compound libraries and screening3 Genomics3 Preclinical and clinical studies3 Sequencing3 Virology3 Data quality management2 DNA mutation2 Exome sequencing2 Gene transcripts2 Quantitative genetics2 Rare diseases2 Sequence analysis2 Biological databases1 Biomedical science1 Data integration and warehousing1 DNA packaging1 DNA polymorphism1 Drug discovery1 Epigenomics1 Gene expression1 Metabolomics1 Metatranscriptomics1 Microbiology1 Protein folds and structural domains1 Proteomics1 Structural genomics1 More...

Sequencing quality control9 Variant calling8 Sequence assembly7 Sequence clustering6 Variant filtering6 Sequence alignment5 De-novo assembly4 Haplotype mapping3 Sequence assembly validation3 Genome assembly2 Indel detection2 SNP detection2 Transcriptome assembly2 Variant classification2 Antimicrobial resistance prediction1 Conversion1 Differential gene expression profiling1 Enrichment analysis1 Expression analysis1 Gene expression profiling1 Genetic mapping1 Genome analysis1 Genome comparison1 ID mapping1 Mapping1 Metabolic pathway prediction1 Phasing1 Sequence assembly visualisation1 Sequence contamination filtering1 Sequence cutting1 Sequence trimming1 Taxonomic classification1 Validation1 More...

Stable147 Work-in-progress57