M. tuberculosis Variant Analysis tutorial

Annotation: M. tuberculosis Variant Analysis

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: FastQC
Output dataset 'output' from step 1
select at runtime
select at runtime
select at runtime
False
Not available.
7
Step 7: FastQC
Output dataset 'output' from step 2
select at runtime
select at runtime
select at runtime
False
Not available.
7
Step 8: Trimmomatic
Paired-end (two separate input files)
Output dataset 'output' from step 2
Output dataset 'output' from step 1
False
Trimmomatic Operations
Trimmomatic Operation 1
Sliding window trimming (SLIDINGWINDOW)
4
30
Trimmomatic Operation 2
Drop reads below a specified length (MINLEN)
20
Step 9: MultiQC
Results
Results 1
FastQC
FastQC outputs
FastQC output 1
Raw data
Output dataset 'text_file' from step 6,Output dataset 'text_file' from step 7
Empty.
Empty.
False
False
Step 10: Kraken2
Paired
Output dataset 'fastq_out_r1_paired' from step 8
Output dataset 'fastq_out_r2_paired' from step 8
True
0.0
0
True
False
Create Report:
True
False
False
2019-07-14T163343Z_standard_kmer-len_35_minimizer-len_31_minimizer-spaces_6
Step 11: snippy
Use a genome from history and build index
Output dataset 'output' from step 3
Paired
Output dataset 'fastq_out_r1_paired' from step 8
Output dataset 'fastq_out_r2_paired' from step 8
Advanced parameters:
60
10
0.1
100.0
Empty.
Empty.
False
The final annotated variants in VCF format A simple tab-separated summary of all the variants The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.
Step 12: TB Variant Filter
Output dataset 'snpvcf' from step 11
Filter out variants by regions Filter variants close to indels Filter sites by read alignment depth
No
Step 13: TB-Profiler Profile
Illumina
BAM
Output dataset 'snpsbam' from step 11
Text
Yes
bwa
10
0.1
0.1
Step 14: Text transformation
Output dataset 'output1' from step 12
s/GENE_//g
Hide Advanced Options
Step 15: JBrowse
Use a genome from history
Output dataset 'output' from step 5
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 11
True
5000000
JBrowse Custom Track Config [Advanced]:
Custom Track Config Options
On for new users
No - Do not Override
No - Do not Override
Track Group 2
variants
Annotation Tracks
Annotation Track 1
VCF SNPs
Output dataset 'output1' from step 12
JBrowse Custom Track Config [Advanced]:
Custom Track Config Options
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 Features
Output dataset 'output' from step 4
False
True
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 Custom Track Config [Advanced]:
Custom Track Config Options
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:
True
False
False
Empty.
Step 16: TB Variant Report
Output dataset 'output' from step 14
Output dataset 'results_json' from step 13
True
Advanced options:
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