Galaxy | CPT Public | Accessible Workflow | PAP 2017 Structural (v8.8)

PAP 2017 Structural (v8.8)

Annotation:

Step	Annotation
Step 1: Input dataset input select at runtime
Step 2: Remove Description Fasta file Output dataset 'output' from step 1
Step 3: 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 4: MetaGeneAnnotator fasta Output dataset 'out' from step 2
Step 5: GeneMarkS Input FASTA sequence Output dataset 'out' from step 2 Output format GFF2 Genome Phage
Step 6: 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 7: 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 No value found for 'Full gene model for GFF3 data'. Using default: 'False'.
Step 8: Glimmer3 to GFF3 Glimmer Output Output dataset 'prediction' from step 3 Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2
Step 9: MGA to GFF3 MGA Output Output dataset 'output' from step 4 Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2
Step 10: Reformat GFF3 File GFF3 Annotations Output dataset 'outfile' from step 5
Step 11: GFF3 Add Gene to CDS GFF3 Annotations Output dataset 'out_gff3_file' from step 6
Step 12: Fix tRNA model GFF3 Annotations Output dataset 'gff3_output_file' from step 7
Step 13: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'data' from step 8 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 14: GFF3 Feature Type Filter GFF3 Annotations Output dataset 'data' from step 9 Feature Types Feature Types 1 Feature type Shine_Dalgarno_sequence Invert the filter True	MGA has substandard RBS annotations so we ignore them.
Step 15: TransTermHP Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'data' from step 9
Step 16: Regex Find And Replace Select lines from Output dataset 'default' from step 10 Checks Check 1 Find Regex gene_id= Replacement ID=
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 11
Step 18: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 13 Remove 'remark' features True Remove 'region' features True No value found for 'Remove 'region' features'. Using default: '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 14 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 20: Correct GeneMarkS Gene Model GFF3 Annotations Output dataset 'out_file1' from step 16
Step 21: 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 22: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 19 Remove 'remark' features True Remove 'region' features True No value found for 'Remove 'region' features'. Using default: 'True'.
Step 23: Shine Find Reference Genome From History Source FASTA Sequence Output dataset 'out' from step 2 GFF3 Annotations Output dataset 'default' from step 20 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 24: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 21 Remove 'remark' features True Remove 'region' features True No value found for 'Remove 'region' features'. Using default: 'True'.
Step 25: Remove Annotation Feature GFF3 Annotations Output dataset 'stdout' from step 23 Remove 'remark' features True Remove 'region' features True No value found for 'Remove 'region' features'. Using default: 'True'.
Step 26: Unknown Tool with id 'jbrowse-cpt'
Step 27: Unknown Tool with id 'edu.tamu.cpt2.webapollo.create_or_update'
Step 28: Unknown Tool with id 'edu.tamu.cpt2.webapollo.iframe'

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PAP 2017 Structural (v8.8)

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