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MultiQC19
SAMtools15
fastp11
gfastats9
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BUSCO7
Cutadapt7
Bowtie 26
BWA6
lofreq6
Minimap26
ggplot25
MACS5
snpEff5
Bandage4
BCFtools4
GenomeScope 2.04
kraken24
Merqury4
QualiMap4
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FASTX-Toolkit3
gffread3
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iVar3
taxonomy_krona_chart3
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biomformat2
bx-python2
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PRINSEQ2
purge_dups2
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ampvis1
anndata1
BLAST1
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Bwa-mem21
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Clair31
Clustal 2 (Clustal W, Clustal X)1
cmsearch-deoverlap1
DeepTools1
DESeq21
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eggNOG-mapper v21
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GOseq1
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iqtree1
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SRA Software Toolkit1
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Genomics9
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single-cell5
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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
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Hi-C2
image-processing2
long-reads2
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Reviewed2
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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
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bwa-mem21
BY-COVID1
cage1
cage-seq1
cageseq-data1
cancer1
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chimeric-alignment1
chromatin-accessibiity1
chromatin-immunoprecipitation1
chromosome-conformation-capture1
circle-seq1
circular1
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clip1
clip-seq1
comparative-genomics1
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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
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diagnostics1
differential-abundance1
dna-methylation1
dot-plot1
download1
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ena1
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ggbio1
gnomad1
google1
gro-seq1
gsea1
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hicar1
hla1
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host-pathogen1
hybrid-assembly1
hyperparameter-tuning1
identification1
image-analysis1
image-segmentation1
imaging1
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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 Bot170
Space
nf-core82
Creator
Paul Zierep5
Wolfgang Maier3
Peter van Heusden1
Pavankumar Videm1
Wolfgang Maier1
Anthony Bretaudeau1
Delphine Lariviere1
Anton Nekrutenko1
Romane Libouban1
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170
Workflows visible to you, out of a total of 170
Type: Nextflow
Creators: Christopher Mohr, Alexander Peltzer, Sven Fillinger
Submitter: WorkflowHub Bot
Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and ...
Decontamination Workflow
Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite.
Inputs
- Genome Assembly [fasta]
- Database for Kraken2. Database containing the possible contaminants.
Ouput
- List of contaminant scaffolds
- List of mitochondrial scaffolds
- Decontaminated assembly
This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.
Type: Nextflow
Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau
Submitter: WorkflowHub Bot
This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.
