All Published Workflows

2 workflows that have been reviewed and published

oecophylla
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Modular Shotgun Sequence Analysis Workflow: Oecophylla - Harnessing Snakemake
public

public

Canonically pronounced ee-co-fill-uh , Oecophylla is a Snakemake wrapper for shotgun sequence analysis. Rather than being...
raw sequence reads Analysis Sequence report scp MEGAHIT Anvio BEDTools Bowtie 2 Centrifuge FastQC HUMAnN2 Kraken Mash MetaQUAST MultiQC Pandas QUAST SAMtools seqtk Snakemake SPAdes SqueezeMeta numpy scikit-bio Sequence analysis
Free
48
phytopipe
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Plant Pathogen Detection Pipeline (PhytoPipe) for RNA-seq Data
public

public

# PhytoPipe: A Phytosanitary Pipeline for plant pathogen detection and diagnosis using RNA-seq data PhytoPipe is an open-sour...
RNA sequence Sequence read processing Sequence report bwakit crass Bowtie 2 BWA cloudSPAdes metaspades MultiQC MUMmer4 plasmidspades QUAST rnaspades RVDB-prot seqtk Snakemake SPAdes Trimmomatic Plant biology RNA-Seq
Free
1