Workflows
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Tool
MultiQC21
SAMtools16
fastp11
gfastats9
BEDTools7
Bowtie 27
BUSCO7
Cutadapt7
BWA6
lofreq6
Minimap26
compleasm5
ggplot25
MACS5
snpEff5
Bandage4
BCFtools4
GenomeScope 2.04
kraken24
Merqury4
QualiMap4
BamTools3
FastQC3
FASTX-Toolkit3
gffread3
Gromacs3
Open Babel3
taxonomy_krona_chart3
ToolDistillator3
AmberTools2
anndata2
biomformat2
bx-python2
Cufflinks2
iVar2
JBrowse2
MAPseq2
MaxQuant2
Medaka2
Meryl2
PRINSEQ2
purge_dups2
QUAST2
RDKit2
seqtk2
STAR2
StringTie2
Trimmomatic2
Workflow4Metabolomics2
xcms2
ABRicate1
ampvis1
Bakta1
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BLAST1
Bracken1
Bwa-mem21
CheckM1
ChemicalToolbox1
Clair31
Clustal 2 (Clustal W, Clustal X)1
cmsearch-deoverlap1
CONCOCT1
CoverM1
dastool1
DeepTools1
DESeq21
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edgeR1
eggNOG-mapper v21
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GOseq1
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iqtree1
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MetaBAT 21
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msConvert1
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shovill1
snipit1
SRA Software Toolkit1
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Metagenomics10
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nanopore7
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Proteomics5
single-cell5
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bacterial-genomics4
covid-194
illumina4
microbiome4
openms4
taxonomic-profiling4
10xgenomics3
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ARTIC3
ATAC-seq3
covid19.galaxyproject.org3
denovo-assembly3
DNA3
genome-assembly3
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mass-spectrometry3
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taxonomic-classification3
10x-genomics2
adna2
Alignment2
AMR2
antibiotic-resistance2
antimicrobial-resistance-genes2
ChIP-seq2
demultiplexing2
differential-expression2
eDNA2
fasta2
GATK42
Hi-C2
image-processing2
long-reads2
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nanopore-sequencing2
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ONT2
pacbio2
paired-end2
peak-calling2
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proteogenomics2
quality2
quantification2
shotgun2
star-solo2
structural-variants2
taxonomy-assignment2
training2
transcriptome2
Transcriptomics2
Virus2
WGS2
#single-cell1
16S1
18S1
airr1
alevin1
alphafold21
alternative-splicing1
amp1
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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
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clip1
clip-seq1
comparative-genomics1
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contigs1
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coprolite1
corruption1
cosmic1
covid191
cramtofastq1
crispr1
crispr-analysis1
crispr-cas1
cross-validation1
ctat1
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cutandrun-seq1
cutandtag1
cutandtag-seq1
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cytometry1
data-cleaning1
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demo1
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deseq21
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dot-plot1
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ena1
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google1
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isoseq-31
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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
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
taxonomies1
tidyverse1
tmt1
transcription1
transcriptional-dynamics1
tree1
trend-analysis1
trends1
trimming1
tss1
ultra1
umi1
umis1
unique-molecular-identifier1
unpaired-reads1
variant-annotation1
vgp1
viral1
viral-integration1
Virology1
viruses1
virusintegrationfinder1
well-formed1
wes1
whole-exome-sequencing1
whole-genome-alignment1
whole-genome-sequencing1
worflow1
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Submitter
WorkflowHub Bot176
Space
nf-core84
Creator
Paul Zierep6
Wolfgang Maier3
Peter van Heusden1
Pavankumar Videm1
Wolfgang Maier1
Anthony Bretaudeau1
Delphine Lariviere1
Anton Nekrutenko1
Bérénice Batut1
Romane Libouban1
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176
Workflows visible to you, out of a total of 176
Perform background subtraction, nuclear segmentation, feature quantification, cellular phenotyping, spatial analysis, and interactive visualization of registered TMA core multiplex tissue images
This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps. ...
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Type: Nextflow
Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer
Submitter: WorkflowHub Bot
Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses Kraken2 to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.
Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.
