All Published Workflows

8 workflows that have been reviewed and published

dna-seq-neoantigen-prediction
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Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
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This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sam...
Sequence Genetic variation analysis genetic variants gatk hla-la rust-bio-tools tabix Arriba BCFtools BWA Cutadapt FreeBayes kallisto Microphaser NetMHCIIpan NetMHCpan Pandas Picard Quant razers3 SAMtools Snakemake STAR Strelka Variant Effect Predictor (VEP) vembrane Jinja2 numpy Varlociraptor Genomics
Free
122
hribo
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HRIBO: High-throughput annotation by Ribo-seq workflow for analyzing bacterial Ribo-seq data
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public

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of ...
Sequence Sequence annotation ORF ID gatk ucsc-bigwigtowig BEDTools Cutadapt FastQC FeatureCounts GFFutils MultiQC Picard SAMtools Snakemake wigToBigWig bacterial assembly and annotation
Free
154
rnasplice
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rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
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public

nf-core/rnasplice is a bioinformatics pipeline for alternative splicing analysis of RNA sequencing data obtained from orga...
Sequence Alternative splicing prediction RNA sequence bioconductor-tximeta misopy rmats ucsc-bedclip umi_tools bedGraphToBigWig BEDTools DESeq DRIMSeq FastQC FeatureCounts gffread HTSeq MultiQC Quant RSEM Salmon SAMtools stageR STAR SUPPA Trim_Galore RNA splicing
Free
79
scrnaseq
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A single-cell RNAseq pipeline for 10X genomics data
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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
qc-of-radseq-reads
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Quality Control of RAD-seq reads on the Galaxy platform
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public

workflow-qc-of-radseq-reads These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using...
FASTQ Sequence Sequencing quality control Sequence Cutadapt fastp FastQC Galaxy MultiQC Stacks WorkflowHub Population genomics
Free
purge-duplicates-from-hifiasm-assembly-v1-0
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Purge duplicates from hifiasm assembly v1.0
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public

Please see the Genome assembly with hifiasm on Galaxy Australia guide. The workflow & the doc_guidelines template used ar...
FASTQ Sequence Genome assembly Sequence alignment Sequence cutting File name Galaxy Minimap2 purge_dups WorkflowHub Sequence assembly
Free
sars-cov-2-pe-illumina-artic-ivar-analysis-sars-co
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COVID-19 sequence analysis on Illumina Amplicon PE data
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public

COVID-19 sequence analysis on Illumina Amplicon PE data sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLIC...
File format name Sequence Sequence analysis Sample ID nextclade usher BWA fastp Galaxy iVar MultiQC nextstrain.org Pangolin QualiMap SAMtools snpEff WorkflowHub Sequence analysis
Free
gatk4-fastq-to-joint-called-cohort-vcf-with-cromwe
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Fastq to Joint-Called Cohort VCF Pipeline with GATK4 and Cromwell on SLURM
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public

SLURM HPC Cromwell implementation of GATK4 germline variant calling pipeline See the GATK website for more information on...
BAM VCF Sequence Variant calling File format name gatk BWA dbSNP Picard SAMtools Genomics
Free
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