Microbial Variant Calling (imported from URL)

Annotation: Microbial Variant Calling

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Input dataset
select at runtime
Step 5: Input dataset
select at runtime
Step 6: snippy
Output dataset 'output' from step 4
Paired
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Advanced parameters:
60
10
0.9
Empty.
Empty.
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
Use a genome from history
Output dataset 'output' from step 3
True
11. The Bacterial, Archaeal and Plant Plastid Code
New JBrowse Instance
Track Groups
Track Group 1
sequence reads
Annotation Tracks
Annotation Track 1
BAM Pileups
Output dataset 'snpsbam' from step 6
True
On for new users
No - Do not Override
No - Do not Override
Track Group 2
variants
Annotation Tracks
Annotation Track 1
GFF/GFF3/BED/GBK Features
Output dataset 'snpgff' from step 6
False
False
Canvas Features
CanvasFeatures Options [Advanced]:
Empty.
Empty.
False
JBrowse Styling Options [Advanced]:
feature
product,name,id
note,description
10px
600
JBrowse Feature Score Scaling & Coloring Options [Advanced]:
Ignore score
Automatically selected
JBrowse Contextual Menu options [Advanced]:
Track Menus
On for new users
No - Do not Override
No - Do not Override
Track Group 3
annotated reference
Annotation Tracks
Annotation Track 1
GFF/GFF3/BED/GBK Features
Output dataset 'output' from step 5
False
False
Canvas Features
CanvasFeatures Options [Advanced]:
Empty.
Empty.
False
JBrowse Styling Options [Advanced]:
feature
product
product
10px
600
JBrowse Feature Score Scaling & Coloring Options [Advanced]:
Ignore score
Automatically selected
JBrowse Contextual Menu options [Advanced]:
Track Menus
On for new users
No - Do not Override
No - Do not Override
General JBrowse Options [Advanced]:
Empty.
20
True
Empty.
True
True
True
True
False
Plugins:
False
False
False
Default
Empty.