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SnakeLines 0.9.2 documentation
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Table of Contents
User documentation
Quick start
Running SnakeLines
Configuration of a pipeline
Useful bash aliases
Developer notes
Source code structure
Developing new rules
Replace default methods
How to write documentation
Pipelines
Read quality report
Preprocess sequencing reads
Map reads to a reference genome
Download reference and map reads
Assemble reads
Call variants
Analyse methylation profiles
Analyse gene expression
Analyse microbial composition
Identify viruses
Download reference
Infer phylogeny between genomic sequences
Documentation
Rules
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SnakeLines 0.9.2 documentation
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