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Merge pull request #114 from Plant-Food-Research-Open/genemark/lic
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Added GeneMark license info
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GallVp authored Nov 21, 2024
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## Introduction

**plant-food-research-open/genepal** is a bioinformatics pipeline for single genome, phased genomes and pan-genome annotation. An overview is shown in the [Pipeline Flowchart](#pipeline-flowchart) and the references for the tools are listed in [CITATIONS.md](./CITATIONS.md).
**plant-food-research-open/genepal** is a bioinformatics pipeline for single genome, phased genomes and pan-genome annotation. An overview is shown in the [Pipeline Flowchart](#pipeline-flowchart) and the references for the tools are listed in [CITATIONS.md](./CITATIONS.md). Protein coding gene structures are predicted with [BRAKER](https://github.com/Gaius-Augustus/BRAKER) which uses GeneMark-ES/ET/EP+/ETP. These tools require a [license](https://genemark.bme.gatech.edu/license_download.cgi) for commercial works.

## Pipeline Flowchart

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- [sra-tools](https://github.com/ncbi/sra-tools): RNASeq data download from SRA
- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc), [fastp](https://github.com/OpenGene/fastp), [SortMeRNA](https://github.com/sortmerna/sortmerna): QC, trim and filter RNASeq evidence
- [STAR](https://github.com/alexdobin/STAR): RNASeq alignment
- Directly provided BAM files should be `--outSAMstrandField intronMotif` compliant
- [cat](https://github.com/coreutils/coreutils/blob/master/src/cat.c): Concatenate protein FASTA files
- [BRAKER](https://github.com/Gaius-Augustus/BRAKER): Annotate the genome FASTA
- [BRAKER](https://github.com/Gaius-Augustus/BRAKER): Predict protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS
- Directly provided BAM files should be `--outSAMstrandField intronMotif` compliant
- With protein evidence alone, [BRAKER workflow C](https://github.com/Gaius-Augustus/BRAKER/tree/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471?tab=readme-ov-file#overview-of-modes-for-running-braker) is executed
- With protein plus RNASeq evidence, [BRAKER workflow D](https://github.com/Gaius-Augustus/BRAKER/tree/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471?tab=readme-ov-file#overview-of-modes-for-running-braker) is executed
- [Liftoff](https://github.com/agshumate/Liftoff): Optionally, liftoff annotations from reference genome FASTA/GFF
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