Viral genome notebook
Building consensus genome from raw fastq reads
Configure notebook for run
Prepare sample list
Load required python libraries
Fetch fastq files from SRA
Sub-sample reads for binder run
Check for viral DNA contamination using Fastv
Fetch required reference genomes and list of unique k-mers
Prepare function for fastv run
Run fastv for all samples
De-novo assembly of viral genome using Megahit
Prepare function for Megahit assembly run
Run de-novo assembly for all the samples
Map raw reads on reference genome
Prepare function for reference genome fetching
Build Bowtie2 index for reference genome
Prepare function for bowtie2 mapping
Run bowtie2 mapping for all the samples
Consensus genome building from mapped reads
Prepare function for consensus fasta building
Run consensus fasta building for all samples
Multiple sequence alignment and tree building
Data fetching
Multiple sequence alignment with Muscle
Tree building using FastTree
Plotting trees
Referenc
Tree building for 153 Coronavirus genomes
Fetch data
Build phylogenetic tree with FastTree
Plot trees
Reference
Alignment and tree building using Nextstrain
Introduction
Configure notebook for run
Load required python libraries
Fetch genome sequences
Multiple sequence alignment and tree building
Metadata configs for Nextstrain
Nextstrain visualization
References
Viral genome notebook
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Viral genome analysis notebooks
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Viral genome analysis notebooks
¶
A repo for keeping notebooks for viral genome analysis and data visualization
List of example notebooks
¶
Building consensus genome from raw fastq reads
Multiple sequence alignment and tree building
Tree building for 153 Coronavirus genomes
Alignment and tree building using Nextstrain
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