{"repo":"nf-core/genomeannotator","free":true,"listed":false,"github":"https://github.com/nf-core/genomeannotator","clone":"git clone https://github.com/nf-core/genomeannotator.git","description":"Pipeline for the identification of (coding) gene structures in draft genomes.","language":"Nextflow","stars":41,"topics":["nf-core","nextflow","workflow","pipeline","genome-annotation","gene-annotation","annotation","draft-genome","assembly","genome-assembly"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/genomeannotator is a bioinformatics best-practice analysis pipeline for the annotation of eukaryote genomes. It was developed with a focus on metazoans - although other groups should work as well. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! Pipeline summary 1. Preprocess assembly (filter out small contigs, clean sequence names) 2. Align evidences (proteins, transcripts, RNAseq) 3. Convert alignments to annotation support 4. Build gene models using AUGUSTUS and optionally PASA 5. Compute consensus gene build using EvidenceModeler Optional steps include de-novo transcriptome assembly (Trinity) and annotation mapping from related genomes (Satsuma2 and Kraken). Quick Start 1. Install Nextflow ( =21.10.3 ) 2. Install any of Docker , Singularity , Podman , Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs) 3. Download the pipeline and test it on a minimal dataset with a single","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/genomeannotator/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}