All Published Workflows

5 workflows that have been reviewed and published

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
antenna
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Carotenoid Antenna Workflow for Energy Transfer in Rhodopsin Pumps
public

public

This is the snakemake workflow behind the paper Chazan et al (2022) "Energy transfer in ubiquitous rhodopsin pumps wi...
APE Biopython CAR castor ggtree hmmalign (genouest) hmmbuild (genouest) hmmsearch (genouest) lme4 MAFFT API (EBI) seqkit Snakemake treeio trimAl dplyr dunn.test emmeans ggnewscale ggplot2 ggpubr phangorn photobiology phytools readxl seqinr tidyr crc64iso Plant biology
Free
41
1-plant-virus-detection-with-kraken2-se
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Plant virus detection with kraken2 (SE)
public

public

Metagenomic dataset taxonomic classification using kraken2
Galaxy kraken2 Krona WorkflowHub Plant biology Taxonomy
Free
1-plant-virus-detection-with-kraken2-pe
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Plant virus detection with kraken2 (PE)
public

public

Metagenomic dataset taxonomic classification using kraken2
Galaxy kraken2 Krona WorkflowHub Infectious disease Plant biology
Free
0-view-complete-virus-identification
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Comprehensive view on plant virus classification.
public

public

Non-functional workflow to get a global view of possibilities for plant virus classification.
elastic-blast BLAST fastp FLASH Galaxy kraken2 Minimap2 NGSUtils Picard shovill WorkflowHub Plant biology viral-genomics
Free