Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
Fpocket1
MultiQC67
FastQC58
SAMtools55
fastp47
BUSCO35
BWA34
Minimap231
anndata27
Bowtie 227
Cutadapt26
BEDTools24
SCANPY24
ggplot222
Bandage21
kraken220
BLAST19
QUAST19
BCFtools18
gfastats17
Merqury16
taxonomy_krona_chart15
JBrowse14
seqtk14
SRA Software Toolkit14
MACS13
scikit-learn13
Bwa-mem212
GenomeScope 2.012
gffread12
NanoPlot12
STAR12
Trimmomatic12
BamTools11
FreeBayes11
mothur11
StringTie11
DeepTools10
Flye10
Open Babel10
DESeq29
Galaxy Image Analysis9
HISAT29
lofreq9
MaxQuant9
Stacks9
Trim Galore9
UniProt9
msConvert8
R8
scikit-image8
Unicycler8
Biopython7
bx-python7
FASTX-Toolkit7
Galaxy7
MaBoSS7
MAFFT7
PhysiCell7
purge_dups7
Racon7
RSeQC7
shovill7
snpEff7
GEMINI6
Gromacs6
KrakenTools6
MuSiC Deconvolution6
QualiMap6
RDKit6
RepeatMasker6
Seurat6
TransDecoder6
Vcflib6
antiSMASH5
Bracken5
compleasm5
DropletUtils5
FeatureCounts5
GOseq5
iqtree5
Konstanz Information Miner (KNIME)5
Medaka5
MEGAHIT5
Scipion5
seqkit5
SPAdes5
Unipept5
annotatemyids4
CellProfiler4
Clustal 2 (Clustal W, Clustal X)4
COMBAT-TB Workbench4
Cufflinks4
Diamond4
funannotate4
Galactic Circos4
gffcompare4
InterProScan (EBI)4
Meryl4
MSstats4
Newick Utilities4
NGSUtils4
PretextView4
Salmon4
Smudgeplots4
snippy4
Workflow4Metabolomics4
xcms4
ABRicate3
AmberTools3
Bakta3
Cardinal3
ChiRA3
cisTEM3
compute_sequence_length3
eggNOG-mapper v23
Falco3
FastTree3
HiCExplorer3
HUMAnN23
Infernal3
MAKER3
MAPseq3
MetaNovo3
MetaPhlAn3
metaspades3
MotionCor23
MSstatsTMT3
Nextflow3
OMArk3
picard_samtofastq3
Prokka3
pyGenomeTracks3
Recentrifuge3
SeqCode3
staramr3
tb-profiler3
ToolDistillator3
UMI-tools3
VarScan3
Variant Effect Predictor (VEP)3
YaHS3
AutoDock2
AutoDock Vina2
BBMap2
bed to protein map2
Bio3D2
BioContainers2
biomformat2
BRAKER12
cBioPortal2
CheckM2
ChEMBL2
chemfp2
ChemicalToolbox2
Clair32
clusterProfiler2
CNVkit2
cshl_fastx_reverse_complement2
customProDB2
edgeR2
EGA2
epiScanpy2
FEELnc2
Filtlong2
GATK2
GOEnrichment2
Helixer2
Hifiasm2
humann2
Integron Finder2
ISEScan2
iVar2
limma2
Matchms2
MaxBin2
MDAnalysis2
MEME2
MetaBAT 22
metaQuantome2
MFAssignR2
miniasm2
nanopolish2
NCBI Datasets2
NCBI Resources2
OBITools2
P2Rank2
The Protein Data Bank (PDB)2
Picard2
pilon2
PlasmidFinder2
PredPrIn2
PRINSEQ2
Prodigal2
Proteinortho2
QIIME2
RepeatModeler2
sceasy2
Scipion-chem2
SemiBin2
Snakemake2
SnapATAC2
SnpSift2
SuCOS2
tbl2gff32
tophat22
VADR2
vardict2
vcfanno2
vcfutils2
VSEARCH2
XMIPP2
AdapterRemoval1
AGAT1
ampvis1
AnnotSV1
Apollo1
AUGUSTUS1
AutoSite1
Binette1
Bioconductor1
BlobToolKit1
blockbuster1
Bowtie1
BRAKER31
CARNIVAL1
ChIPpeakAnno1
Circos1
Clustal 1.8 (Clustal W, Clustal X)1
cmsearch-deoverlap1
CONCOCT1
CoverM1
cuffdiff1
dada21
dastool1
decoupleR1
DeepVariant1
Delly21
diaPASEF1
dRep1
EGSEA1
EMBOSS1
European Nucleotide Archive (ENA)1
ete1
ewastools1
export2graphlan1
FGENESH1
fgsea1
FLASH1
FlashLFQ1
Foldseek1
FREEC1
GADES1
GAEVAL1
gblocks1
GBMatch - GBMPredictor1
GECKO1
GetOrganelle1
ggtree1
g:Profiler1
GraPhlAn1
GSEA1
GTDB-Tk1
hAMRonization1
Heinz1
HiFiAdapterFilt1
htseqcount1
HTSlib1
The Immune Epitope Database (IEDB)1
ImageJ21
IsoformSwitchAnalyzeR1
IWTomics1
JBrowse 21
kraken-biom1
Krona1
LASTZ1
lotus21
MAGeCK1
MALDIquant1
Mash1
MethylDackel1
miniprot1
miRDeep21
MitoHiFi1
MITOS1
MOB-suite1
MolMeDB1
Metagenomic operational taxonomic units (mOTUs)1
MSMetaEnhancer1
multiGSEA1
MUMmer1
mzToSQLite1
ngsReports1
OptiType1
pangolin1
pathview1
Peakachu1
PEAR1
PfamScan1
phyloseq1
PhysiBoSS1
PlasFlow1
PLINK1
Polypolish1
progeny1
protexcluder1
PubMed1
pyfastaq1
PyTorch1
qcxms1
QuickTree1
RaceID1
RAMClustR1
RapidNJ1
RAxML1
RCAS1
recetox-msfinder1
RED1
RepeatModeler1
RIAssigner1
rnaQUAST1
SALSA1
scater1
Seq2HLA1
SeqSero21
sinto1
SISTR1
SNAP1
snipit1
SortMeRNA1
Subread1
tabix1
Targetfinder.org1
TaxonKit1
TRANSIT1
trimAl1
Trinity1
Trinotate1
TSSr1
UCSC Genome Browser Utilities1
VAPOR1
varlociraptor1
varVAMP1
VelvetOptimiser1
WGCNA1
WoLF PSORT1
xtb1
More...
Workflow type
Scipion1
Tag
Bioinformatics1
Cheminformatics1
Consensus1
Drug design1
drug discovery1
Python1
scipion1
Virtual Drug Screening1
Workflows1
More...
Submitter
Daniel Del Hoyo1
Team
Scipion CNB1
Space
Independent Teams1
This workflows contains a pipeline in Scipion that performs the following steps:
1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands
1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.
2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.
2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...