All Published Workflows

5 workflows that have been reviewed and published

taxprofiler
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Highly parallelised multi-taxonomic profiling of shotgun and long-read metagenomic data
public

public

nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shot...
DNA sequence Gene expression profiling Feature table bracken porechop AdapterRemoval BBMap Bowtie 2 Centrifuge Diamond Falco fastp FastQC Filtlong Kaiju kraken2 KrakenUniq Krona MEGAN Metagenomic operational taxonomic units (mOTUs) MetaPhlAn Minimap2 MultiQC Nextflow SAMtools Malt Sequence analysis
Free
62
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
v-pipe-main-multi-virus-version
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V-pipe (main multi-virus version) workflow designed for the analysis of (NGS) data from viral pathogens.
public

public

V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a n...
DNA sequence consensusfixer indelfixer BWA Consensus Vicuna Sequence analysis
Free
42
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