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Tool
MultiQC19
SAMtools14
fastp11
BEDTools8
gfastats8
BUSCO7
Cutadapt7
Bowtie 26
BWA6
lofreq6
ggplot25
MACS5
Minimap25
snpEff5
Bandage4
BCFtools4
GenomeScope 2.04
kraken24
Merqury4
QualiMap4
FastQC3
FASTX-Toolkit3
gffread3
Gromacs3
iVar3
taxonomy_krona_chart3
ToolDistillator3
AmberTools2
BamTools2
biomformat2
bx-python2
Cufflinks2
JBrowse2
MAPseq2
MaxQuant2
Medaka2
Open Babel2
PRINSEQ2
purge_dups2
RDKit2
STAR2
StringTie2
Trimmomatic2
ABRicate1
ampvis1
anndata1
BLAST1
Bracken1
Bwa-mem21
ChemicalToolbox1
Clair31
Clustal 2 (Clustal W, Clustal X)1
cmsearch-deoverlap1
DESeq21
edgeR1
eggNOG-mapper v21
FastTree1
FEELnc1
Flye1
FreeBayes1
GOseq1
Helixer1
Infernal1
Integron Finder1
InterProScan (EBI)1
iqtree1
ISEScan1
KrakenTools1
MAFFT1
MAKER1
MetaNovo1
msConvert1
MSstats1
NanoPlot1
Newick Utilities1
OMArk1
PlasmidFinder1
QUAST1
Recentrifuge1
SCANPY1
SeqCode1
seqtk1
shovill1
snipit1
SRA Software Toolkit1
SuCOS1
Unipept1
UniProt1
VAPOR1
Vcflib1
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Genomics9
Metagenomics9
rna8
nanopore7
rna-seq7
variant-calling7
Proteomics6
Assembly5
ChIP5
FASTQ5
single-cell5
ABRomics4
bacterial-genomics4
covid-194
illumina4
microbiome4
openms4
10xgenomics3
Annotation3
ARTIC3
ATAC-seq3
covid19.galaxyproject.org3
denovo-assembly3
DNA3
genome-assembly3
long-read-sequencing3
mass-spectrometry3
Metabolomics3
RNASEQ3
taxonomic-classification3
taxonomic-profiling3
10x-genomics2
adna2
Alignment2
AMR2
antibiotic-resistance2
antimicrobial-resistance-genes2
ChIP-seq2
demultiplexing2
differential-expression2
eDNA2
fasta2
GATK42
GTN2
Hi-C2
image-processing2
long-reads2
Metabarcoding2
MS2
nanopore-sequencing2
NGS2
ONT2
pacbio2
paired-end2
peak-calling2
proteogenomics2
quality2
quantification2
Reviewed2
shotgun2
star-solo2
structural-variants2
taxonomy-assignment2
training2
transcriptome2
Transcriptomics2
vgp2
Virus2
WGS2
workflow4metabolomics2
#single-cell1
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
cancer1
cell-lines1
Cellranger1
chimeric-alignment1
chromatin-accessibiity1
chromatin-immunoprecipitation1
chromosome-conformation-capture1
circle-seq1
circular1
Classification1
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
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
epigenome1
Epigenomics1
epitope1
epitope-prediction1
eukaryotes1
evolution1
evolutionary-tree1
extrachromosomal-circular-dna1
facs-sorting1
fair-principles1
fastq-corrupted1
fastq-format1
FastQC1
filter1
fish1
function1
fusion1
fusion-genes1
GC-MS1
gene-expression1
gene-fusion1
generalization1
generic1
genome1
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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
immunorepertoire1
imputation1
iontorrent1
isoseq1
isoseq-31
ITS1
iwc1
k-mer1
kallisto1
kmer1
kmer-counting1
kmer-frequency-count1
kraken21
krona1
label-free-quantification1
landsat1
last1
LC-MS1
lfq1
limma1
linked-reads1
long-read1
low-pass-sequencing1
machine-learning1
macs21
mapping1
MARS-seq1
mass-spec1
metagenomes1
metaMS1
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
pangenome1
pathogen1
pathogen-genomics1
pbat1
peptides1
personalized-medicine1
phasing1
phylogenetic-placement1
phylogenetics1
phylogeny1
pixelator1
pixelgen-technologies1
population-genetics1
pox1
pre-processing1
pro-seq1
Profiling1
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
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
taxonomies1
tidyverse1
tmt1
transcription1
transcriptional-dynamics1
tree1
trend-analysis1
trends1
trimming1
tss1
ultra1
umi1
umis1
unique-molecular-identifier1
unpaired-reads1
variant-annotation1
viral1
viral-integration1
Virology1
viruses1
virusintegrationfinder1
well-formed1
wes1
whole-exome-sequencing1
whole-genome-alignment1
whole-genome-sequencing1
worflow1
xcms1
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Submitter
WorkflowHub Bot168
Space
nf-core82
Creator
Paul Zierep5
Wolfgang Maier3
Peter van Heusden1
Pavankumar Videm1
Wolfgang Maier1
Anthony Bretaudeau1
Anton Nekrutenko1
Romane Libouban1
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168
Workflows visible to you, out of a total of 168
Tests 
This workflow uses eggNOG mapper and InterProScan for functional annotation of protein sequences.
This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.
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
This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.
