Rules

• Paired End

  • Classification

    • Viral

      • Undocumented rules

      • Identification

        • Virfinder - Identify Viral Sequences

    • Report

      • Transcripts

        • Pca

          • Sklearn - Pca Comparison

        • Count Table

          • Custom - Summarize Transcriptomic Counts Into Tsv Table

        • Revigo

          • Custom - Export De Genes For Revigo

        • Html Table

          • Custom - Visualise Transcriptomic Counts In Html Table

      • Taxonomic Counts

        • Pieplot

          • Krona - Single Sample Pieplot
          • Krona - Multi Sample Pieplot

        • Barplot

          • Custom - Visualise Taxonomic Counts As Barplot

        • Alpha Diversity

          • Custom - Alpha Diversity

        • Count Table

          • Custom - Summarize Taxonomic Counts Into Tsv Table
          • Custom - Extract Taxonomic Level From Taxonomic Table

      • Summary

        • Fasta_Summary - Blast
        • Fasta_Summary - Coverage
        • Fasta_Summary - Mapped Reads
        • Fasta_Summary - Copy Contigs
        • Fasta_Summary - Summarize Annotations
        • Undocumented rules

    • Contig Based

      • Blast - Find Homologues
      • Blast - Annotate With Taxonomy
      • Blast - Prepare Reference Index For Nucleotide
      • Blast - Prepare Reference Index For Protein

    • Transcripts

      • Salmon - Classify Reads
      • Salmon - Create Reference Index
      • Salmon - Prepare For Krona

    • Differential Analysis

      • Edger - Identify Transcripts With Changed Expression
      • Edger - Convert Summary Tsv Table To Xlsx

      • Filter Significant

        • Custom - Filter Significantly Expressed Transcripts

    • Read Based

      • Fast_Virome_Explorer - Estimate Virome Composition
      • Custom - Fill Na Values With Virusnames
      • Custom - Convert To Tpm Metric
      • Custom - Convert To Krona
      • Metaxa2 - Classify Reads
      • Metaxa2 - Create Reference Index
      • Metaxa2 - Summarize Classification
      • Metaxa2 - Prepare For Krona
      • Rdp - Classify Reads
      • Rdp - Prepare For Krona

  • Mapping

    • Mapper

      • Bwa - Map Reads To Reference
      • Bismark - Map Methyl Seq Reads To Reference
      • Bowtie2 - Map Reads To Reference

  • Assembly

    • Report

      • Quality Report

        • Quast - Quality Report For Assembled Contigs

      • Assembly Graph

        • Bandage - Visualise Contig Overlaps

    • Assembler

      • Megahit - Assemble Reads Into Contigs
      • Megahit - Generate Contig Graph
      • Spades - Assemble Reads Into Contigs
      • Unicycler - Assemble Reads Into Contigs

  • Reads

    • Report

      • Quality Report

        • Fastqc - Html Summary For Joined Reads
        • Fastqc - Html Summary For Paired Reads
        • Fastqc - Quality Report

    • Preprocess

      • Joined

        • Pear - Join Read Pairs
        • Pear - Concat Joined With Single

      • Deduplicated

        • Fastuniq - Deduplicate Reads

      • Decontaminated

        • Bowtie2 - Filter Reads From Reference

      • Subsampled

        • Seqtk - Subsample Reads

      • Trimmed

        • Trimmomatic - Trim Reads

• Shared

  • Consensus

    • Caller

      • Bcftools - Build Consensus Sequence

  • Mapping

    • Report

      • Quality Report

        • Qualimap - Mapping Quality Report Across Reference
        • Qualimap - Mapping Quality Report Across Panel
        • Qualimap - Summarize Quality Reports

      • Methylation

        • Bismark - Methylation Extractor
        • Bismark - Summary Report

    • Postprocess

      • Deoverlapped

        • Custom - Remove Overlapping Reads

      • Read Group

        • Custom - Infer Read Groups

      • Deduplicated

        • Picard - Mark Duplicates

      • Sorted

        • Samtools - Sort Mapped Reads

      • Realigned

      • Filtered

        • Bamtools - Filter Fragments

    • Merged

      • Bamtools - Merge Bams Into Single Bam File

    • Index

      • Samtools - Convert Sam To Bam
      • Samtools - Bam Index

    • Mapper

      • Indices

        • Bowtie2 - Prepare Index
        • Bwa - Prepare Index
        • Bismark - Prepare Index

  • Reference

    • Report

      • Phylogenetic Tree

        • Phylo - Visualise Phylogenetic Tree

      • Comparison

        • Msaviewer - Visualise Alignment

    • Download

      • Entrez - Download Sequences By Genbank Id

    • Alignment

      • Mafft - Align Sequences In Reference

    • Attributes

      • Desc

        • Custom - Prepare Description File

    • Index

      • Dict

        • Picard - Prepare Dict Index

      • Fai

        • Samtools - Prepare Fai Index

    • Phylogeny

      • Iqtree - Infer Phylogeny

  • Variant

    • Report

      • Summary

        • Custom - Summary Report

      • Calling

        • Gatk - Fix Vcf Header
        • Tabix - Index Vcf
        • Picard - Bed To Interval List
        • Gatk - Collect Variant Calling Metrics

    • Caller

      • Vardict - Create Wgs Bed File
      • Vardict - Prepare Bed File
      • Vardict - Call Germline Variants
      • Vardict - Test Strand Bias
      • Vardict - Tsb To Vcf
      • Clair - Variant Call Mapped Reads
      • Vcfcat - Merge Vcf Files
      • Medaka - Variant Call Mapped Reads
      • Freebayes - Variant Call Mapped Reads

  • Reads

    • Preprocess

      • Conversion

        • Pigz - Unzip File

• Single End

  • Mapping

    • Mapper

      • Minimap2 - Map Reads To Reference
      • Bowtie2 - Map Reads To Reference

  • Reads

    • Report

      • Quality Report

        • Fastqc - Html Summary For Joined Reads
        • Fastqc - Html Summary For Paired Reads
        • Fastqc - Quality Report

    • Preprocess

      • Decontaminated

        • Bowtie2 - Filter Reads From Reference

      • Trimmed

        • Trimmomatic - Trim Reads