Workflows

FastQC5 SAMtools5 Stacks5 MultiQC4 Minimap23 QUAST3 Bandage2 BUSCO2 BWA2 Bwa-mem22 fastp2 Racon2 Trimmomatic2 VSEARCH2 Cutadapt1 Flye1 GenomeScope 2.01 HiFiAdapterFilt1 Medaka1 Merqury1 NanoPlot1 PEAR1 picard_samtofastq1 purge_dups1 More...

Galaxy130 Common Workflow Language51 Nextflow27 Jupyter18 Python15 Snakemake13 Shell Script11 Bpipe5 KNIME5 Workflow Description Language5 PyCOMPSs3 Scipion2 Janis1 R markdown1 More...

covid-1942 Assembly21 Alignment15 INDELs13 SNPs13 CWL12 Galaxy12 Genomics12 Nextflow12 workflow12 RNASEQ11 GATK49 Large-genome-assembly9 Metagenomics9 rna9 rna-seq9 variant_calling9 cancer8 Transcriptomics8 Annotation7 scalable7 covid19.galaxyproject.org6 ONT6 PBS6 vgp6 bpipe5 Climate5 groovy5 illumina5 NCI5 pediatric5 Bioinformatics4 copernicus4 FASTQ4 Gadi4 generic4 Retrosynthesis4 SAMTools4 variant calling4 Virology4 WGS4 ARTIC3 BWA3 ChIP3 Classification3 Default-SDR3 DNA3 HiFi3 image processing3 kraken3 MetaDEGalaxy3 mirna prediction3 NCI-Gadi3 Pathway Analysis3 pathway prediction3 protein3 Proteomics3 rare diseases3 scRNA-seq3 STAR3 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 manta2 mapping2 metabolic engineering2 Metabolomics2 molecular dynamics2 mpxv2 multi-specimen-input2 MultiQC2 nanopore2 nf-core2 pathway design2 phylogenetics2 phylogenomics2 PyCOMPSs2 QC2 Semantic Network Analysis2 Snakemake2 structural variants2 Synthetic Biology2 Tophat22 TransBioNet2 trinity2 validated-2022-06-292 VARSCAN22 VCF2 WDL2 10X1 18S1 ABR1 abricate1 air-quality1 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 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 HaplotyeCaller1 HTSeq1 humann21 imaging1 index1 ITS1 Juicer1 LiftOver1 Machine Learning1 map1 MapSplice1 MARS-seq1 mass-spectrometry1 memote1 Merqury1 Meryl1 Metabarcoding1 metagenome1 microbial1 miRanda1 mlxv1 model1 Modeling1 mpvx1 Multi-omics1 Mutect21 name:ONT1 NCI Gadi1 ndvi1 networks1 non-coding1 non-model1 nonspliced1 observation1 openebench1 pangenome1 pangeo1 parallel1 pathogenicity score1 Pfam1 Pipeline1 Presence_absence1 prokka1 Protein domains1 purge_dups1 quality1 quantification1 Quast1 radio interferometry1 reads_selection1 reads_simulation1 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 Somatic1 SPARK1 Species abundance1 Statistics1 strandedness1 StringTie1 Supernova1 SV1 TAD1 TargetScan1 tcga1 TELLSeq1 topologically associating domains1 Toxicology1 trajectories1 transcriptome1 tumour1 Unicycler1 variant pathogenicity prediction1 variant-analysis1 variation1 Virus1 whole genome sequencing1 Workflows1 More...

Genís Bayarri38 WorkflowHub Bot23 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 Martin Beracochea3 Yvan Le Bras3 Irene Sánchez3 Georgina Samaha3 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 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 More...

BioBB Building Blocks48 Australian BioCommons29 iwc23 GalaxyProject SARS-CoV-221 Galaxy Australia21 UNLOCK13 Sydney Informatics Hub12 usegalaxy-eu11 Galaxy Climate8 IBISBA Workflows7 CWL workflow SARS-CoV-26 MGnify5 IMBforge5 UX trial team5 Integrated and Urban Plant Pathology Laboratory5 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-wings-EU1 BCCM_ULC1 More...

Independent Teams125 BioExcel48 Australian BioCommons40 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 Chew10 Laura Rodriguez-Navas9 Rosemarie Sadsad9 José Mª Fernández6 Georgina Samaha6 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 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 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 More...

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 BioCommons ‘Bring Your Own Data’ Expansion Project4 IDR3 Vertebrate Genomes Pipelines (VGP) workflows3 TronFlow2 More...

Sequence assembly16 Genetic variation9 Population genomics9 Whole genome sequencing8 Metagenomics6 Bioinformatics4 Metagenomic sequencing4 Compound libraries and screening3 Preclinical and clinical studies3 Sequencing3 Transcriptomics3 Virology3 Data quality management2 Exome sequencing2 Gene transcripts2 Genomics2 Quantitative genetics2 Rare diseases2 Sequence analysis2 Biological databases1 Biomedical science1 Data integration and warehousing1 DNA mutation1 DNA packaging1 DNA polymorphism1 Drug discovery1 Epigenomics1 Gene expression1 Metabolomics1 Microbiology1 Protein folds and structural domains1 Proteomics1 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...

Stable144 Work-in-progress54