Galaxy | CPT Public | Accessible Workflow | Modified PAP Structural Workflow v.2020.06 for updating existing organism

Modified PAP Structural Workflow v.2020.06 for updating existing organism

Annotation: For updating existing organism (need to have the retrieved retrieve JSON first)

Step	Annotation
Step 1: Input dataset Input Sequence select at runtime
Step 2: Remove Description Fasta file Output dataset 'output' from step 1
Step 3: tRNAscan-SE Input Fasta File Output dataset 'out' from step 2 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 4: tRNA and tmRNA Genome Sequence Output dataset 'out' from step 2 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 5: Glimmer3 Genome sequence Output dataset 'out' from step 2 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 6: MetaGeneAnnotator fasta Output dataset 'out' from step 2
Step 7: Get open reading frames (ORFs) or coding sequences (CDSs) Sequence file (nucleotides) Output dataset 'out' from step 2 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) 30 Strand to search Search both the forward and reverse strand
Step 8: Convert tRNAscan-SE table to gff format tRNAscan table Output dataset 'default' from step 3
Step 9: Fix tRNA model GFF3 Annotations Output dataset 'gff3_output_file' from step 4
Step 10: Glimmer3 to GFF3 Glimmer Output Output dataset 'prediction' from step 5 Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2
Step 11: MGA to GFF3 MGA Output Output dataset 'output' from step 6 Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2
Step 12: GFF3 Add Gene to CDS GFF3 Annotations Output dataset 'out_gff3_file' from step 7
Step 13: Fix tRNA model GFF3 Annotations Output dataset 'output' from step 8
Step 14: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'data' from step 10 Minimum number of bases upstream of CDS for gap (--lookahead_min) 5 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 15: TransTermHP Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'data' from step 11
Step 16: GFF3 Feature Type Filter GFF3 Annotations Output dataset 'data' from step 11 Feature Types Feature Types 1 Feature type Shine_Dalgarno_sequence Invert the filter True
Step 17: GFF3 Filter: Require Phage Start Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'output' from step 12
Step 18: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 14 Remove 'remark' features True Remove 'region' features True
Step 19: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'output' from step 16 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 20: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'stdout' from step 17 Minimum number of bases upstream of CDS for gap (--lookahead_min) 5 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: Prep GFF3 Input for Apollo GFF3 Annotations Output dataset 'default' from step 18
Step 22: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 19 Remove 'remark' features True Remove 'region' features True
Step 23: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 20 Remove 'remark' features True Remove 'region' features True
Step 24: Prep GFF3 Input for Apollo GFF3 Annotations Output dataset 'default' from step 22
Step 25: GFF3 Add Gene to CDS for Sixpack GFF3 Annotations Output dataset 'default' from step 23
Step 26: Prep GFF3 Input for Apollo GFF3 Annotations Output dataset 'output' from step 25
Step 27: JBrowse Reference genome to display Use a genome from history Select the reference genome Output dataset 'out' from step 2 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 / Official Annotation Tracks Annotation Track 1 Track Type GFF/GFF3/BED Features GFF/GFF3/BED Track Data Output dataset 'output' from step 24,Output dataset 'output' from step 21 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 / Gene Calls / Naive Annotation Tracks Annotation Track 1 Track Type GFF/GFF3/BED Features GFF/GFF3/BED Track Data Output dataset 'output' from step 26 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 3 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 'default' from step 13,Output dataset 'output' from step 15,Output dataset 'default' from step 9 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 28: Create or Update Organism JBrowse HTML Output Output dataset 'output' from step 27 Organism Common Name Source Autodetect from Apollo JSON Apollo Organism File select at runtime 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 29: Annotate Apollo Organism Listing Output dataset 'output' from step 28 Force the tracklist on in JBrowse False

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Modified PAP Structural Workflow v.2020.06 for updating existing organism

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