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SnakeLines 1.1.8 documentation
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Index
Table of Contents
User documentation
Quick start
Running SnakeLines
Configuration of a pipeline
Useful bash aliases
Additional tools
Developer notes
Source code structure
Developing new rules
Replace default methods
How to write documentation
Pipelines
Read quality report
Preprocess sequencing paired-end reads
Map paired-end reads to a reference genome
Download reference and map paired-end reads
Assemble reads
Call variants
Analyse methylation profiles
Analyse gene expression
Analyse microbial composition
Identify viruses
Download reference
Infer phylogeny between genomic sequences
Analyse single-end Illumina samples
Analyse variants from nanopore reads
Variant detection in SARS-CoV-2
Documentation
Rules
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SnakeLines 1.1.8 documentation
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