Annotation pipeline

This Annotation pipeline is an automatic structural annotation workflows written in snakemake. The annotation is based on two tools which uses RNA-Seq and/or protein homology information for predict coding sequence. One of this tools is BRAKER [ref & lien] which use GeneMark-EX [ref] and AUGUSTUS [ref]. And the other tool is Augustus [ref] alone for improve annotation of small coding sequences with few or no intron.

Mandatory installation

• Hisat2

• samtools

• exonerate

• BRAKER

• BUSCO

• R & Rmarckdown package**

• Python >=3.7

• Snakemake >= 5.2

Prepare config file

To run the workflows you have to provide the data path for all input file. Please complete the config.yaml file for launch the workflow.

1. Providing data

{
        "datadir"   : "/homedir/user/work/Masked_assembly/",
        "OutDir"    : "/homedir/user/work/pipeline_output/",
        "RnaSeqDir" : "/homedir/user/work//rnaseq/",
        "id_souche" : "magnaporthe_oryzae",
        "protRef"   : "/homedir/user/work/Annotation_pipeline/SupplementaryFile/OG_filter.fasta"
}

• datadir : Path of you directory which contain all your fasta file to annotate.

• RnaSeqDir : Path of the directory which contain all RNAseq data,

• id_souche : ID of species for augustus trainings, please refers to augustus main page for this option

• protRef : Path of the protein fasta file.

• OutDir : Output directory for all results of this pipeline

Launching on a single machine

To launch this annotation pipeline on a single machine, please use the command :

snakemake -s annotation_pipeline.snake --latency-wait 555555

2. Launching on HPC clusters

Preparing cluster configuration using cluster_config.yaml

On cluster_config.yaml, you can add partition, memory and to be used by default for each rule. This pipeline is used on cirad HPC [link], so the environment (module load command) and sge submission works only on the cirad cluster. Please adapt the content of this file before running on a cluster with your cluster parameters or if you need more memory for a rules.

Here is a example of the configuration file we used on the Cirad HPC.

__default__:
  n_cpu: "-pe parallel_smp"
  mem: "-l mem_free=4G"
  export_env: "-V"
  cwd: "-cwd"
  logerror: "-e "
  log: "-o "
  queue: " -q long.q"
  scheduler: "qsub"

###### Cluster parameters for hisat2_index rules ########
hisat2_index :
  mem: "-l mem_free=4G"
  queue: " -q normal.q"

Launch workflows

For launch the pipeline in a cluster please use the Launcher.sh give in the directory.