Egzotek

Egzotek is a bioinformatic pipeline designed for transcript annotation of non-model species with incomplete or poorly annotated genomes. It is developed to build a consensus annotated genome usig long RNA reads.

1. Read orientation
   1. Oriented protocol (eoulsan)
   2. Non-oriented protocol (restrander)
2. Transcript annotation with RNA-Bloom
   1. Transcript annotation (rna-bloom) (with optional short-read polishing)
   2. Genome mapping (minimap2)
   3. Bam to bed file conversion (minimap2-paftools)
   4. Bed to gff file conversion (agat)
   5. Gff to gtf file conversion (agat)
3. Transcript annotation with Isoquant
   1. Genome mapping (minimap2)
   2. Sam to bam file conversion (samtools)
   3. Transcript annotation (isoquant)
4. Complement annotation (agat)
5. Clusterisation (gffread)
6. Merge annotation

Installing Egzotek

$ git clone [email protected]:GenomiqueENS/egzotek.git
$ cd egzotek

Configuration

Customize runs by editing the nextflow.config file and/or specifying parameters at the command line.

Usage

$ nextflow run transcript_annotation.nf

Pipeline Input Parameters

Here are the primary input parameters for configuring the workflow:

Parameter	Description	Default Value
reads	Path to the fastq files (required)	test_data/*.fasta
samplesheet	Path to the samplesheet file (required)	test_data/samplesheet.csv
genome	Path to the genome .fasta file (required)	test_data/Treesei_QM6a.fasta
annotation	Path to the reference transcriptome .gtf file (required)	test_data/transcriptome.gtf
oriented	Orientation of reads based on library protocol (required)	false
sam	Path to sam files after eoulsan (required if oriented=true)	null

Tools Parameters

Configuration of tools used for annotation process:

Parameter	Description	Default Value
config	Path to Restrander configuration file (TSO and RTP sequences) (required if reads are non oriented)	/assets/PCB111.json
intron_length	Parameter for maximum intron length for Minimap2	20000
junc_bed	Parameter for junction bed annotation for Minimap2	null
model_strategy	Parameter for transcript model construction algorithm	default_ont
optional_shortread	Path to Illumina shortreads .fasta file for RNA-Bloom	null

Additional Parameters

Parameter	Description	Default Value
outdir	Output directory for results	"result"

Run Parameters

Configuration for running the workflow:

Parameter	Description	Default Value
threads	Number of threads to use	4
docker.runOptions	Docker run options to use	'-u $(id -u):$(id -g)'

Results

After execution, results will be available in the specified --outdir. This includes SAM and BAM files produced for IsoQuant and RNABloom and gtf with annotated transcriptomes.

Cleaning Up

To clean up temporary files generated by Nextflow:

nextflow clean -f

Support and Contributions

For support, please open an issue in the repository's "Issues" section. Contributions via Pull Requests are welcome. Follow the contribution guidelines specified in CONTRIBUTING.md.

License

Egzotek is distributed under a specific license. Check the LICENSE file in the GitHub repository for details.