Galaxy | CPT Public | Accessible Workflow | PAP Structural Workflow v2021.01

PAP Structural Workflow v2021.01

Annotation: Structural Phage annotation workflow, please see the guide at https://cpt.tamu.edu/training-material/topics/phage-annotation-pipeline/ for help

Step	Annotation
Step 1: Input parameter Organism Name Not available.
Step 2: Input dataset Input Sequence select at runtime
Step 3: Remove Description Fasta file Output dataset 'output' from step 2
Step 4: tRNAscan-SE Input Fasta File Output dataset 'out' from step 3 tRNA model to use Bacterial Cutoff score (in bits) for reporting tRNAs 20 Number of nucleotide padding when passing first-pass tRNA bounds predictions to CM analysis 8 Run search without HMM filter False Disable pseudogene checking False
Step 5: tRNA and tmRNA Genome Sequence Output dataset 'out' from step 3 Genetic code 11. Bacteria and Archaea Topology Assume that each sequence has a circular topology Search for tmRNA genes True Search for tRNA genes True Search for Metazoan mitochondrial tRNA genes False Search for Mammalian mitochondrial tRNA genes False Search for tRNA genes with introns in anticodon loop False Print out secondary structure False Convert output to GFF3 True Full gene model for GFF3 data False
Step 6: Glimmer3 Genome sequence Output dataset 'out' from step 3 Set maximum overlap length. Overlaps this short or shorter are ignored. 30 Set minimum gene length. 20 Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene. 30 Assume linear rather than circular genome, i.e., no wraparound True Output a detailed gene prediction report as separate file True Report the classic glimmer table output True
Step 7: MetaGeneAnnotator fasta Output dataset 'out' from step 3
Step 8: Get open reading frames (ORFs) or coding sequences (CDSs) Sequence file (nucleotides) Output dataset 'out' from step 3 Genetic code 11. Bacterial Look for ORFs or CDSs Look for CDSs (with start and stop codons) Minimum length ORF/CDS (in amino acids, e.g. 30 aa = 90 bp plus any stop codon) 25 Strand to search Search both the forward and reverse strand
Step 9: Convert tRNAscan-SE table to gff format tRNAscan table Output dataset 'default' from step 4
Step 10: Fix tRNA model GFF3 Annotations Output dataset 'gff3_output_file' from step 5
Step 11: Glimmer3 to GFF3 Glimmer Output Output dataset 'prediction' from step 6 Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3
Step 12: MGA to GFF3 MGA Output Output dataset 'output' from step 7 Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3
Step 13: GFF3 Add Gene to CDS GFF3 Annotations Output dataset 'out_gff3_file' from step 8
Step 14: Fix tRNA model GFF3 Annotations Output dataset 'output' from step 9
Step 15: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3 GFF3 Annotations Output dataset 'data' from step 11 Minimum number of bases upstream of CDS for gap (--lookahead_min) 3 Maximum number of bases upstream of CDS for gap (--lookahead_max) 17 Automatically add RBSs to input GFF3 True Only report best hits (--top_only) True
Step 16: TransTermHP Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3 GFF3 Annotations Output dataset 'data' from step 12
Step 17: GFF3 Feature Type Filter GFF3 Annotations Output dataset 'data' from step 12 Feature Types Feature Types 1 Feature type Shine_Dalgarno_sequence Invert the filter True
Step 18: GFF3 Filter: Require Phage Start Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3 GFF3 Annotations Output dataset 'output' from step 13
Step 19: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 15 Remove 'remark' features True Remove 'region' features True
Step 20: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3 GFF3 Annotations Output dataset 'output' from step 17 Minimum number of bases upstream of CDS for gap (--lookahead_min) 3 Maximum number of bases upstream of CDS for gap (--lookahead_max) 17 Automatically add RBSs to input GFF3 True Only report best hits (--top_only) True
Step 21: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 3 GFF3 Annotations Output dataset 'stdout' from step 18 Minimum number of bases upstream of CDS for gap (--lookahead_min) 3 Maximum number of bases upstream of CDS for gap (--lookahead_max) 17 Automatically add RBSs to input GFF3 True Only report best hits (--top_only) True
Step 22: Prep GFF3 Input for Apollo GFF3 Annotations Output dataset 'default' from step 19
Step 23: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 20 Remove 'remark' features True Remove 'region' features True
Step 24: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 21 Remove 'remark' features True Remove 'region' features True
Step 25: Prep GFF3 Input for Apollo GFF3 Annotations Output dataset 'default' from step 23
Step 26: GFF3 Add Gene to CDS for Sixpack GFF3 Annotations Output dataset 'default' from step 24
Step 27: Prep GFF3 Input for Apollo GFF3 Annotations Output dataset 'output' from step 26
Step 28: JBrowse Reference genome to display Use a genome from history Select the reference genome Output dataset 'out' from step 3 Produce Standalone Instance False Genetic Code 11. The Bacterial, Archaeal and Plant Plastid Code JBrowse-in-Galaxy Action New JBrowse Instance Track Groups Track Group 1 Track Category #date# Structural Annotation / Gene Calls Annotation Tracks Annotation Track 1 Track Type GFF/GFF3/BED Features GFF/GFF3/BED Track Data Output dataset 'output' from step 25,Output dataset 'output' from step 22,Output dataset 'output' from step 27 This is match/match_part data False Maximum size of track chunks 2000000 Index this track False JBrowse Track Type [Advanced] Neat Canvas Features CanvasFeatures Options [Advanced]: Transcript type Empty. Subfeatures type Empty. Implied UTRs False JBrowse Styling Options [Advanced]: JBrowse style.className feature JBrowse style.label product,name,id JBrowse style.description note,description JBrowse style.height 10px JBrowse maxHeight 600 JBrowse Feature Score Scaling & Coloring Options [Advanced]: Color Score Algorithm Ignore score Color Selection Automatically selected JBrowse Custom Track Config [Advanced]: Custom Track Config Options JBrowse Contextual Menu options [Advanced]: Track Menus Track Visibility Off for new users Override Apollo Plugins No - Do not Override Override Apollo Draggability No - Do not Override Track Group 2 Track Category #date# Structural Annotation / Sequence Analysis Annotation Tracks Annotation Track 1 Track Type GFF/GFF3/BED Features GFF/GFF3/BED Track Data Output dataset 'output' from step 16,Output dataset 'default' from step 14,Output dataset 'default' from step 10 This is match/match_part data False Maximum size of track chunks 2000000 Index this track False JBrowse Track Type [Advanced] Neat Canvas Features CanvasFeatures Options [Advanced]: Transcript type Empty. Subfeatures type Empty. Implied UTRs False JBrowse Styling Options [Advanced]: JBrowse style.className feature JBrowse style.label product,name,id JBrowse style.description note,description JBrowse style.height 10px JBrowse maxHeight 600 JBrowse Feature Score Scaling & Coloring Options [Advanced]: Color Score Algorithm Ignore score Color Selection Automatically selected JBrowse Custom Track Config [Advanced]: Custom Track Config Options JBrowse Contextual Menu options [Advanced]: Track Menus Track Visibility Off for new users Override Apollo Plugins No - Do not Override Override Apollo Draggability No - Do not Override General JBrowse Options [Advanced]: Default Location Empty. Track Padding 20 Enable Share Link True About the Browser Empty. Show Track List True Show Navigation True Show Overview True Show Menu True Hide Genome Options False Plugins: BlastView True Combo Track Selector False GC Content False None Empty.
Step 29: Create or Update Organism JBrowse HTML Output Output dataset 'output' from step 28 Organism Common Name Source Direct Entry Organism Common Name (Required) Not available. Genus Empty. Species Empty. Is Organism Public False Grant access to a user group None Remove old data directory False Update genome sequences False None no
Step 30: Annotate Apollo Organism Listing Output dataset 'output' from step 29 Force the tracklist on in JBrowse False

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PAP Structural Workflow v2021.01

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