MGKit: Metagenomic framework
0.3.2
Introduction
Installation
Metagenomic Pipeline
Tutorial
HMMER Tutorial
Profile a Community with BLAST
Gene Prediction
Scripts Details
Example Notebooks
MGKit GFF Specifications
Library Reference
Changes
MGKit: Metagenomic framework
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Metagenomic Pipeline
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Metagenomic Pipeline
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This section detailed information about example pipelines made using the framework
Tutorial
Initial setup
Getting Sequence Data
Taxonomy Data
Metagenome Assembly
Gene Prediction
Using BLAST
Using RAPSearch
Create the GFF
Taxonomic Refinement
Complete GFF
Alignment
Coverage and SNP Info
SNP Calling
SAMtools
Data Preparation
Diversity Analysis
Count Data
Additional Downloads
IPython Notebook
Full Bash Script
Explore Data Python Script
HMMER Tutorial
Requirements
Metagenomic Data
Digital Normalisation and QC
Assembly
Download Data
Create Profiles
Alignment and HMM profiles
Gene Prediction
GFF Creation
GFF Filtering
GFF Additions
Alignments
Coverage and Expected SNPs
SNP Calling
IPython Notebook
Full Bash Script
Explore Data Python Script
Profile a Community with BLAST
Considerations
Requirements
MacOS X
Download Data
Assembly
NCBI nt
ID to Taxonomy
NCBI Taxonomy
Community Profiling
BLAST
Convert into a GFF
Adding the Taxonomic Information
Filter the GFF
Getting the Profile
Gene Prediction
Prediction Software
General Procedure
Functional Prediction
Generate Profiles
Filter Annotations
Taxonomic Prediction
Last Common Ancestor
Complete Annotations
Examples
Gene Prediction with BLAST+
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v: 0.3.2
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