Galaxy | Europe | Accessible Workflow | Microbial Variant Calling (imported from URL)

Microbial Variant Calling (imported from URL)

Annotation: Microbial Variant Calling

Step	Annotation
Step 1: Input dataset mutant_R1 select at runtime
Step 2: Input dataset mutant_R2 select at runtime
Step 3: Input dataset wildtype.fna select at runtime
Step 4: Input dataset wildtype.gbk select at runtime
Step 5: Input dataset wildtype.gff select at runtime
Step 6: snippy Reference File (either in fasta or genbank format) Output dataset 'output' from step 4 Single or Paired-end reads Paired Select first set of reads Output dataset 'output' from step 1 Select second set of reads Output dataset 'output' from step 2 Advanced parameters: Minimum mapping quality 60 Minimum coverage 10 Minumum proportion for variant evidence 0.9 Bam header @RG ID Empty. Extra BWA MEM options Empty. Output selection The final annotated variants in VCF format The variants in GFF3 format A simple tab-separated summary of all the variants A summary of the samples and mapping A log file with the commands run and their outputs A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants) A version of the reference genome with all variants instantiated Output of samtools depth for the .bam file The alignments in BAM format. Note that multi-mapping and unmapped reads are not present. Zipped files needed for input into snippy-core
Step 7: JBrowse Reference genome to display Use a genome from history Select the reference genome Output dataset 'output' from step 3 Produce Standalone Instance True Genetic Code 11. The Bacterial, Archaeal and Plant Plastid Code JBrowse-in-Galaxy Action New JBrowse Instance Track Groups Track Group 1 Track Category sequence reads Annotation Tracks Annotation Track 1 Track Type BAM Pileups BAM Track Data Output dataset 'snpsbam' from step 6 Autogenerate SNP Track True Track Visibility On for new users Override Apollo Plugins No - Do not Override Override Apollo Draggability No - Do not Override Track Group 2 Track Category variants Annotation Tracks Annotation Track 1 Track Type GFF/GFF3/BED/GBK Features GFF/GFF3/BED Track Data Output dataset 'snpgff' from step 6 This is match/match_part data False Index this track False JBrowse Track Type [Advanced] 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 Contextual Menu options [Advanced]: Track Menus Track Visibility On for new users Override Apollo Plugins No - Do not Override Override Apollo Draggability No - Do not Override Track Group 3 Track Category annotated reference Annotation Tracks Annotation Track 1 Track Type GFF/GFF3/BED/GBK Features GFF/GFF3/BED Track Data Output dataset 'output' from step 5 This is match/match_part data False Index this track False JBrowse Track Type [Advanced] 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 JBrowse style.description product JBrowse style.height 10px JBrowse maxHeight 600 JBrowse Feature Score Scaling & Coloring Options [Advanced]: Color Score Algorithm Ignore score Color Selection Automatically selected JBrowse Contextual Menu options [Advanced]: Track Menus Track Visibility On 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: Combo Track Selector False Bookmarks False GC Content False JBrowse Theme Default None Empty.

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jenj

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