snakeMake

Overview

This repository contains a collection of Snakemake workflows and supporting scripts for genomics and transcriptomics analysis, designed for use on SGE or SLURM clusters (e.g., VSC). The pipelines cover a range of tasks including genome assembly, annotation, RNA-seq analysis, chimeric RNA detection, and more.

Features

• Multiple Genome Alignment: Automated workflows for aligning multiple genomes and extracting conserved elements.
• De Novo Genome Assembly: Pipelines for assembly using Newbler and MIRA.
• Genome Annotation: Automated annotation using evidence-based and ab initio methods (in progress).
• Chimeric RNA Extraction: Identify chimeric RNAs from STAR-mapped reads.
• Functional Annotation: Annotate predicted proteins with InterProScan, MEROPS, CAZy, TCDB, and more.
• Differential Expression: Identify differentially expressed genes from RNA-seq count data.
• lncRNA Discovery: Pipeline for long non-coding RNA identification and quantification.

Requirements

• Snakemake
• Python 3.x
• R (with edgeR, limma, optparse, etc.)
• Perl (for some utility scripts)
• Cluster environment (SGE or SLURM recommended)
• Bioinformatics tools: STAR, Trinity, Cufflinks, PASA, Augustus, SNAP, InterProScan, BLAST, bedtools, featureCounts, RepeatMasker, etc.

See each workflow for specific dependencies.

Usage

Each workflow is defined in a .Snakemake file. To run a workflow:

snakemake -d $(pwd) -s $(pwd)/<workflow>.Snakemake --stats snakemake.stats -j <jobs> --cluster 'qsub <cluster_params>'

Replace <workflow> with the desired pipeline (e.g., genomeAnnotation, differentialExpression, chimericRNA, etc.).

Workflow Descriptions

Below is a summary of each main workflow, with typical inputs and outputs. See the top of each .Snakemake file for more details and required file formats.

genomeAnnotation.Snakemake

• Purpose: Automated genome annotation using ab initio and evidence-based methods (e.g., PASA, Trinity, Cufflinks, Augustus, SNAP, Scipio, CEGMA).
• Input: Genome FASTA, RNA-seq reads, protein databases.
• Output: Annotated GFF/GTF files, intermediate files for each tool.

differentialExpression.Snakemake

• Purpose: Differential gene expression analysis from RNA-seq count data.
• Input: FeatureCounts or similar count matrix, sample metadata.
• Output: Lists of differentially expressed genes, summary statistics.

functionalAnnotation.Snakemake

• Purpose: Functional annotation of predicted proteins using InterProScan, MEROPS, CAZy, TCDB, and BLAST.
• Input: Protein FASTA files, annotation databases.
• Output: Annotated TSV/merged files, summary tables.

chimericRNA.Snakemake

• Purpose: Detect and extract chimeric RNAs from STAR-mapped RNA-seq data.
• Input: STAR chimeric junction files, genome FASTA.
• Output: Chimeric RNA lists, GFF/TSV files.

lncRNA.Snakemake

• Purpose: Identify and quantify long non-coding RNAs (lncRNAs) from transcriptome assemblies.
• Input: Genome annotation, transcript assemblies, protein databases, mapped reads.
• Output: lncRNA GFF files, count tables, differential expression results.

multipleGenomeAlignments.Snakemake

• Purpose: Perform multiple genome alignments and extract conserved elements.
• Input: Genome FASTA files for all species.
• Output: Alignment files (MAF, GFF), summary statistics.

Other scripts

• Supporting scripts in Perl and R are used for data processing, statistics, and format conversion. See comments in each script for usage.

Example Commands

Genome Annotation

snakemake -d $(pwd) -s $(pwd)/genomeAnnotation.Snakemake --stats snakemake.stats -j 100 --cluster 'qsub {params.cluster}'

Differential Expression

snakemake -d $(pwd) -s $(pwd)/differentialExpression.Snakemake --stats snakemake.stats -j 100 --cluster 'qsub {params.cluster}'

Functional Annotation

snakemake -d $(pwd) -s $(pwd)/functionalAnnotation.Snakemake --stats snakemake.stats -j 100 --cluster 'qsub {params.cluster}'

Chimeric RNA Extraction

snakemake -d $(pwd) -s $(pwd)/chimericRNA.Snakemake --stats snakemake.stats -j 100 --cluster 'qsub {params.cluster}'

lncRNA Discovery

snakemake -d $(pwd) -s $(pwd)/lncRNA.Snakemake --stats snakemake.stats -j 100 --cluster 'qsub {params.cluster}'

Multiple Genome Alignment

snakemake -d $(pwd) -s $(pwd)/multipleGenomeAlignments.Snakemake --stats snakemake.stats -j 100 --cluster 'qsub {params.cluster}'

Directory Structure

• *.Snakemake — Main Snakemake workflow files for each analysis type
• *.pl, *.R — Supporting scripts (Perl, R)
• InterProscanDictionary.dat — Example annotation dictionary
• README.md — This file

Notes

• Some workflows require editing paths and environment variables to match your cluster setup.
• See comments in each workflow for details on required input files and expected outputs.
• For questions or contributions, please open an issue or pull request.