Research Object Crate for ERGA Protein-coding gene annotation workflow
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created: 2026-03-03T15:16:15.558+01:00
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Workflow RO-Crate Profile
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Sagane Joye-Dind
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Research Object Crate for ERGA Protein-coding gene annotation workflow
imported by: Małgorzata Wolniewicz
author: Sagane Joye-Dind
content size: 91622645
creator: Małgorzata Wolniewicz
date created: 2023-09-13 18:24:50.860910+00:00
date modified: 2024-03-05 12:23:14.184651+00:00
date published: 2023-09-13 18:24:50.860910+00:00
description: # ERGA Protein-coding gene annotation workflow. Adapted from the work of Sagane Joye: https://github.com/sdind/genome_annotation_workflow ## Prerequisites The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: [https://github.com/nextflow-io/nextflow/issues/1659](https://github.com/nextflow-io/nextflow/issues/1659). `conda v 23.7.3` `singularity v 3.7.3` `snakemake v 7.32.3` You will also need to acquire a licence key for Genemark and place this in your home directory with name `~/.gm_key` The key file can be obtained from the following location, where the licence should be read and agreed to: http://topaz.gatech.edu/GeneMark/license_download.cgi ## Workflow The pipeline is based on braker3 and was tested on the following dataset from Drosophila melanogaster: [https://doi.org/10.5281/zenodo.8013373](https://doi.org/10.5281/zenodo.8013373) ### Input data - Reference genome in fasta format - RNAseq data in paired-end zipped fastq format - uniprot fasta sequences in zipped fasta format ### Pipeline steps - **Repeat Model and Mask** Run RepeatModeler using the genome as input, filter any repeats also annotated as protein sequences in the uniprot database and use this filtered libray to mask the genome with RepeatMasker - **Map RNAseq data** Trim any remaining adapter sequences and map the trimmed reads to the input genome - **Run gene prediction software** Use the mapped RNAseq reads and the uniprot sequences to create hints for gene prediction using Braker3 on the masked genome - **Evaluate annotation** Run BUSCO to evaluate the completeness of the annotation produced ### Output data - FastQC reports for input RNAseq data before and after adapter trimming - RepeatMasker report containing quantity of masked sequence and distribution among TE families - Protein-coding gene annotation file in gff3 format - BUSCO s…
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is based on: https://github.com/ERGA-consortium/pipelines/tree/main/annotation/snakemake
license: no-permission
main entity: Snakefile
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cite-as: Sagane Joye-Dind. "Research Object Crate for ERGA Protein-coding gene annotation workflow." ROHub. Sep 13 ,2023. https://w3id.org/ro-id/7019724e-b5a0-4f7e-a7d6-a1baacac85df.

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ro-crate-preview.html
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date created: 2023-09-13 18:24:52.667262+00:00
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hisat.yaml
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date created: 2023-09-13 18:24:52.291405+00:00
date modified: 2023-09-13 18:24:55.832618+00:00
license: no-permission
sd date published: 2023-09-13 18:24:52.291405+00:00
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ERGA Protein-coding gene annotation workflow
conforms to: https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/
author: Sagane Joye-Dind
content size: 562
creator: Sagane Joye-Dind
date created: 2023-09-12 19:29:55+00:00
date modified: 2023-09-13 18:25:04.032738+00:00
description: # ERGA Protein-coding gene annotation workflow. Adapted from the work of Sagane Joye: https://github.com/sdind/genome_annotation_workflow ## Prerequisites The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: [https://github.com/nextflow-io/nextflow/issues/1659](https://github.com/nextflow-io/nextflow/issues/1659). `conda v 23.7.3` `singularity v 3.7.3` `snakemake v 7.32.3` You will also need to acquire a licence key for Genemark and place this in your home directory with name `~/.gm_key` The key file can be obtained from the following location, where the licence should be read and agreed to: http://topaz.gatech.edu/GeneMark/license_download.cgi ## Workflow The pipeline is based on braker3 and was tested on the following dataset from Drosophila melanogaster: [https://doi.org/10.5281/zenodo.8013373](https://doi.org/10.5281/zenodo.8013373) ### Input data - Reference genome in fasta format - RNAseq data in paired-end zipped fastq format - uniprot fasta sequences in zipped fasta format ### Pipeline steps - **Repeat Model and Mask** Run RepeatModeler using the genome as input, filter any repeats also annotated as protein sequences in the uniprot database and use this filtered libray to mask the genome with RepeatMasker - **Map RNAseq data** Trim any remaining adapter sequences and map the trimmed reads to the input genome - **Run gene prediction software** Use the mapped RNAseq reads and the uniprot sequences to create hints for gene prediction using Braker3 on the masked genome - **Evaluate annotation** Run BUSCO to evaluate the completeness of the annotation produced ### Output data - FastQC reports for input RNAseq data before and after adapter trimming - RepeatMasker report containing quantity of masked sequence and distribution among TE families - Protein-coding gene annotation file in gff3 format - BUSCO s…
keywords: Annotation, Genomics, Transcriptomics
license: no-permission
producer: ERGA Annotation
programming language: #snakemake
sd date published: 2023-09-12 19:29:55+00:00
sd publisher: https://about.workflowhub.eu/
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fastqc.yaml
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date modified: 2023-09-13 18:24:55.014153+00:00
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protexcluder.yaml
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date created: 2023-09-13 18:24:52.292399+00:00
date modified: 2023-09-13 18:24:56.003168+00:00
license: no-permission
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uniprot_sprot.fasta.gz
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date created: 2023-09-13 18:24:52.663696+00:00
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license: no-permission
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1_MaskRepeat.smk
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tePSI.yaml
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date created: 2023-09-13 18:24:52.294349+00:00
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trimm.yaml
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date created: 2023-09-13 18:24:52.295311+00:00
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blast.yaml
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date created: 2023-09-13 18:24:52.288353+00:00
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agat.yaml
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samtools.yaml
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gaas.yaml
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2_alignRNA.smk
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README.md
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3_braker.smk
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config.yaml
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Sagane Joye-Dind
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ERGA Annotation
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