Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
MultiQC21
SAMtools16
fastp13
gfastats9
BEDTools7
BUSCO7
BWA7
lofreq7
Bowtie 26
Cutadapt6
kraken26
Minimap26
Compleasm5
ggplot25
QualiMap5
snpEff5
ToolDistillator5
Bandage4
BCFtools4
GenomeScope 2.04
MACS4
Merqury4
BamTools3
Bracken3
FastQC3
FASTX-Toolkit3
gffread3
Gromacs3
Open Babel3
Recentrifuge3
taxonomy_krona_chart3
AmberTools2
anndata2
biomformat2
bx-python2
CheckM2
Cufflinks2
JBrowse2
MAPseq2
MaxQuant2
Medaka2
Meryl2
PRINSEQ2
purge_dups2
QUAST2
RDKit2
seqtk2
STAR2
StringTie2
Trimmomatic2
Workflow4Metabolomics2
xcms2
ABRicate1
ampvis1
iVar1
Bakta1
Binette1
BLAST1
Bwa-mem21
ChemicalToolbox1
Clair31
Clustal 2 (Clustal W, Clustal X)1
cmsearch-deoverlap1
compute_sequence_length1
CONCOCT1
CoverM1
dastool1
DeepTools1
DESeq21
dRep1
edgeR1
eggNOG-mapper v21
FastTree1
FEELnc1
Flye1
FreeBayes1
GOseq1
GTDB-Tk1
Helixer1
Infernal1
Integron Finder1
InterProScan (EBI)1
iqtree1
ISEScan1
iVar1
KrakenTools1
MAFFT1
MAKER1
MaxBin1
MEGAHIT1
MetaBAT 21
MetaNovo1
metaspades1
MFAssignR1
msConvert1
MSstats1
NanoPlot1
Newick Utilities1
OMArk1
PlasmidFinder1
SCANPY1
SemiBin1
SeqCode1
shovill1
snipit1
SRA Software Toolkit1
SuCOS1
Unipept1
UniProt1
VAPOR1
Vcflib1
More...
Tag
Metagenomics10
Genomics9
rna9
nanopore7
rna-seq7
variant-calling7
FASTQ6
single-cell6
Virology6
Assembly5
Proteomics5
ABRomics4
bacterial-genomics4
ChIP-seq4
covid-194
DNA4
illumina4
microbiome4
NGS4
openms4
taxonomic-profiling4
10xgenomics3
Annotation3
ARTIC3
ATAC-seq3
covid19.galaxyproject.org3
denovo-assembly3
genome-assembly3
long-read-sequencing3
mass-spectrometry3
RNASEQ3
taxonomic-classification3
WGS3
10x-genomics2
adna2
Alignment2
AMR2
antibiotic-resistance2
antimicrobial-resistance-genes2
cancer2
ChIP2
demultiplexing2
differential-expression2
eDNA2
fasta2
GATK42
Hi-C2
image-processing2
long-reads2
Metabarcoding2
nanopore-sequencing2
ONT2
pacbio2
paired-end2
peak-calling2
Profiling2
proteogenomics2
quality2
quantification2
shotgun2
star-solo2
structural-variants2
taxonomy-assignment2
training2
transcriptome2
Transcriptomics2
Virus2
16S1
18S1
airr1
alevin1
alphafold21
alternative-splicing1
amp1
Amplicon1
amplicon-sequencing1
ampliconarchitect1
ampliconsuite1
AMR-detection1
ancient-dna1
ancient-dna-analysis1
ancientdna1
antimicrobial resistance1
antimicrobial-peptides1
arg1
atac1
ATACseq1
b-cell1
bacteria1
bacterial1
bacterial-genome-analysis1
bacterial-genomes1
bamtofastq1
bases2fastq1
bcl2fastq1
benchmark1
bgc1
binning1
biosynthetic-gene-clusters1
bisulfite-sequencing1
bustools1
BWA-mem1
bwa-mem21
BY-COVID1
cage1
cage-seq1
cageseq-data1
cell-lines1
Cellranger1
chimeric-alignment1
chromatin-accessibiity1
chromatin-immunoprecipitation1
chromosome-conformation-capture1
circle-seq1
circular1
Classification1
clinical1
clip1
clip-seq1
comparative-genomics1
Consensus1
contigs1
Conversion1
coprolite1
corruption1
cosmic1
covid191
cramtofastq1
crispr1
crispr-analysis1
crispr-cas1
cross-validation1
ctat1
cutandrun1
cutandrun-seq1
cutandtag1
cutandtag-seq1
CUTnRUN1
cytometry1
data-cleaning1
data-independent-proteomics1
data-recovery1
database1
database-builder1
dda1
ddbj1
de-identification1
decontamination1
deep-learning1
deep-variant1
demo1
denovo1
deseq21
dia1
dia-proteomics1
diagnostics1
differential-abundance1
dna-methylation1
dot-plot1
download1
draft1
drug-response1
drug-response-prediction1
drugs1
dualrna-seq1
earth-observation1
eccdna1
ecdna1
elementbiosciences1
em-seq1
emergen_validated1
ena1
epidemiology1
epigenome1
Epigenomics1
epitope1
epitope-prediction1
eukaryotes1
evolution1
evolutionary-tree1
exome1
extrachromosomal-circular-dna1
facs-sorting1
fair-principles1
fastq-corrupted1
fastq-format1
FastQC1
filter1
fish1
function1
fusion1
fusion-genes1
gene-expression1
gene-fusion1
generalization1
generic1
genome1
genome-annotation1
genomics-visualization1
genotype1
geo1
Germline1
ggbio1
gnomad1
google1
gro-seq1
gsea1
HiC1
hicar1
hla1
hla-typing1
horizontal-gene-transfer1
host-pathogen1
hybrid-assembly1
hyperparameter-tuning1
identification1
image-analysis1
image-segmentation1
imaging1
immcantation1
immunology1
immunopeptidomics1
immunorepertoire1
imputation1
iontorrent1
isoseq1
isoseq-31
ITS1
k-mer1
kallisto1
kmer1
kmer-counting1
kmer-frequency-count1
kraken21
krona1
label-free-quantification1
landsat1
last1
lfq1
limma1
linked-reads1
long-read1
low-pass-sequencing1
machine-learning1
macs21
mapping1
MARS-seq1
mass-spec1
Metabolomics1
metagenomes1
metagenomic-profiling1
metatranscriptomics1
methyl-seq1
mhc1
mhc-binding-prediction1
microarray1
minimal-example1
mnase-seq1
molecular-pixelation1
molecularcartography1
mpxv1
ms11
ms21
Multi-omics1
MultiQC1
name:amplicon1
name:single-cell1
nanostring1
nanostringnorm1
nascent1
natural-products1
nucleosome1
nucleosome-maps1
nucleosome-positioning1
optitype1
oxford-nanopore1
pairwise-alignment1
panel1
pangenome1
pathogen1
pathogen-genomics1
pbat1
peptides1
personalized-medicine1
phasing1
phylogenetic-placement1
phylogenetics1
phylogeny1
pixelator1
pixelgen-technologies1
population-genetics1
pox1
pre-processing1
pro-seq1
prokaryotes1
protein-databases1
protein-families1
protein-fold-prediction1
protein-folding1
protein-sequences1
protein-structure1
proteins1
puretarget1
pypgatk1
QC1
qiime21
quantseq1
randomization-tests1
rare-disease1
readmapping1
reads-interleaving1
recovery-tool1
repseq1
Reviewed1
rna-rbp-interactions1
robustness-assessment1
rrbs1
rrna1
SAMTools1
SARS-CoV-21
satellite-imagery1
screening1
scRNA-seq1
secondary-metabolites1
Segmentation1
sequence-classification1
shiny1
short-reads1
single-cell-omics1
single-cell-rna-seq1
slamseq1
small-rna1
smrna-seq1
snv1
Somatic1
spatial1
spectral-unmixing1
splicing1
sra1
Supernova1
synapse1
synteny1
tama1
target-panels1
targeted1
taxonomies1
tidyverse1
tmt1
transcription1
transcriptional-dynamics1
tree1
trend-analysis1
trends1
trimming1
tss1
Tutorial1
ultra1
umi1
umis1
unique-molecular-identifier1
unpaired-reads1
variant-annotation1
vgp1
viral1
viral-integration1
viral-metagenomics1
virus-genomes1
viruses1
virusintegrationfinder1
well-formed1
wes1
whole-exome-sequencing1
whole-genome-alignment1
whole-genome-sequencing1
wigits1
worflow1
wts1
More...
Submitter
WorkflowHub Bot180
Creator
Wolfgang Maier10
Paul Zierep6
Romane Libouban5
Peter van Heusden2
Pierre Marin2
Clea Siguret2
Pavankumar Videm1
Anthony Bretaudeau1
Delphine Lariviere1
Anton Nekrutenko1
Bérénice Batut1
Saim Momin1
Wendi Bacon1
More...
180
Workflows visible to you, out of a total of 180
Tests 
Single-cell RNA-seq workflow with Scanpy and Anndata. Based on the 3k PBMC clustering tutorial from Scanpy. It takes count matrix, barcodes and feature files as input and creates an Anndata object out of them. It then performs QC and filters for lowly expressed genes and cells. Then the data is normalized and scaled. Then PCs are computed to further cluster using louvain algorithm. It also generated various plots of clustering colored with highly ranked genes.
Type: Galaxy
Creators: Pavankumar Videm, Hans-Rudolf Hotz, Mehmet Tekman, Bérénice Batut
Submitter: WorkflowHub Bot
Phasing and imputation pipeline
Workflow for clinical metaproteomics database searching
This workflow will perform taxonomic and functional annotations using Unipept and statistical analysis using MSstatsTMT.
In proteomics research, verifying detected peptides is essential for ensuring data accuracy and biological relevance. This tutorial continues from the clinical metaproteomics discovery workflow, focusing on verifying identified microbial peptides using the PepQuery tool.
From metagenomes to peptides
Type: Nextflow
Creators: Sabrina Krakau, Leon Kuchenbecker and Till Englert
Submitter: WorkflowHub Bot
The workflow begins with the Database Generation process. The Galaxy-P team has developed a workflow that collects protein sequences from known disease-causing microorganisms to build a comprehensive database. This extensive database is then refined into a smaller, more relevant dataset using the Metanovo tool.
