All Published Workflows

11 workflows that have been reviewed and published

snakemake_anvio
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Anvi'o Analysis Workflow Using Snakemake
public

public

snakemake rules for running anvio This Snakefile will run a basic anvi'o analysis of a set of assemblies and a set of sam...
Sequence assembly Analysis Data Anvio Bowtie 2 Centrifuge SAMtools Snakemake Sequence analysis Sequence assembly
Free
12
subsampler
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Epidemiological Data Subsampling Pipeline
public

public

subsampler A pipeline for subsampling genomic data based on epidemiological time series data. If you use this tool in a publi...
Database metadata Sequence read processing Data nextclade Biopython Pandas Snakemake epiweeks numpy pycountry pycountry-convert Genomics
Free
9
rnafusion
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RNA-seq analysis pipeline for detection gene-fusions
public

public

nf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing analysis pipeline with curated li...
Sequence variations Sequence analysis Data gatk squid Arriba Bedops fastp FastQC gtftogenepred kallisto MultiQC Nextflow Picard Pizzly QualiMap Quant SAMtools STAR STAR-Fusion StringTie RNA-Seq Sequence analysis
Free
85
eager
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A fully reproducible and state-of-the-art ancient DNA analysis pipeline
public

public

A fully reproducible and state-of-the-art ancient DNA analysis pipeline . nf-core/eager is a scalable and reproducible...
JSON Sequence trace Genetic variation analysis Data angsd gatk mtnucratio pmdtools preseq vcf2genome AdapterRemoval AMPS BBMap BCFtools BEDTools Bowtie 2 BWA fastp FastQC FreeBayes gatk_realigner_target_creator kraken2 MapDamage MultiQC Picard QualiMap SAMtools Malt DNA Sequence analysis
Free
101
circdna
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Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
public

public

nf-core/circdna is a bioinformatics best-practice analysis pipeline for the identification of extrachromosomal circular DN...
DNA sequence Representative sequence identification Data AmpliconArchitect ampliconclassifier circexplorer2 BEDTools BWA Circle-Map CNVkit FastQC Minimap2 MultiQC Picard SAMBLASTER SAMtools seqtk Unicycler PrepareAA Trim_Galore Whole genome sequencing
Free
61
airrflow
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B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
public

public

** nf-core/airrflow ** is a bioinformatics best-practice pipeline to analyze B-cell or T-cell repertoire sequencing data. It ...
DNA sequence Analysis Data airr changeo r-enchantr Biopython fastp FastQC IgBLAST MultiQC Pandas pRESTO VSEARCH shazam Sequence analysis
Free
54
scrnaseq
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A single-cell RNAseq pipeline for 10X genomics data
public

public

nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data....
Sequence Sequence analysis Data simpleaf alevinQC FastQC gffread kallisto MultiQC Quant Salmon SAMtools STAR UniverSC kallistobustools Genomics Sequence analysis
Free
36
partial-de-novo-workflow-ustacks-only
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Partial de novo workflow: ustacks only
public

public

workflow-partial-ustacks-only These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, usi...
Data Sequence clustering Data Galaxy Stacks WorkflowHub Population genomics
Free
parallel-accession-download-main
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parallel accession download pipeline
public

public

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed ru...
raw sequence reads Analysis Data Galaxy SRA Software Toolkit WorkflowHub Function analysis
Free
mc_covid19like_assembly_reads
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Assembly of SARS-CoV-2 genome performed using Unicycler and the SPAdes assemblers
public

public

MC_COVID19like_Assembly_Reads This WF is based on the official Covid19-Galaxy assembly workflow as available from https://c...
DNA sequence Sequence assembly Data File name Bowtie 2 fastp Galaxy SPAdes Unicycler WorkflowHub Sequence analysis Sequence assembly
Free
population-and-community-metrics-calculation-from
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Population and community metrics calculation from Biodiversity data
public

public

Galaxy-E (ecology.usegalaxy.eu) workflow to calculate species presence / absence, community metrics and compute generalized l...
Biodiversity data Calculation Data Galaxy GLM-PCA WorkflowHub Biodiversity
Free