{"id":18598229,"url":"https://github.com/cmdoret/acastellanii_hybrid_assembly","last_synced_at":"2025-05-16T14:11:07.967Z","repository":{"id":46681727,"uuid":"197636317","full_name":"cmdoret/Acastellanii_hybrid_assembly","owner":"cmdoret","description":"Hybrid genome assembly of Acanthamoeba castellanii. 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The different steps of the pipeline are illustrated below.\nThe analysis is implemented by combining the snakemake workflow system with [singularity containers](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#singularity) and conda environments. Each pipeline step is encapsulated and dependencies are managed automatically.\nAll input reads are downloaded automatically from SRA, based on their accession numbers defined in `units.tsv`. A frozen copy of this repository and its output files are available on the associated [Zenodo record](https://doi.org/10.5281/zenodo.5507417).\n\n#### Dependencies\n\n * python \u003e=3.7\n * singularity \u003e= 3.2\n * conda \u003e= 4.8\n\nPython packages:\n\n * snakemake \u003e= 5.5\n\n#### Usage\n\nThe pipeline can be started using:\n\n```bash\nsnakemake --use-conda -j4\n```\nor\n\n```bash\nsnakemake --use-singularity -j4\n```\nto use singularity instead of conda environments.\n\n#### Pipeline steps\n\nThe pipeline uses 3 types of input data:\n * shotgun Illumina reads\n * Hi-C Illumina reads\n * Oxford Nanopore long reads\n\nAll those reads are automatically downloaded from SRA when running the pipeline.\n\nThe initial assembly is performed with long reads only using Flye. The short reads are then used to polish this assembly using HyPo. The Hi-C scaffolding is done using instagraal, followed by instagraal-polish to fix errors introduced by instagraal.\n\n\u003eTODO: Add quast report at the end of the pipeline\n\nEach rule requiring a third party software pulls a standalone container hosted on dockerhub or quay to work in an isolated environment with a fixed version of the software.\n\n![image](doc/rulegraph.svg)\n\n[detailed version](doc/filegraph.svg)\n\nUnfortunately, instagraal requires access to a GPU with CUDA drivers. It is currently not possible to make it compatible with singularity. This means instagraal has to be installed on the host machine for the scaffolding to work. It can also be run via docker by following instructions on the [official repository](https://github.com/koszullab/instaGRAAL).\n\n### References\nTools used in this pipeline:\n * filtlong v0.2.0: \n * [flye](https://github.com/fenderglass/Flye/) v2.3.6: doi:10.1073/pnas.1604560113\n * [seqtk](https://github.com/lh3/seqtk) v1.3\n * [bowtie2](https://github.com/BenLangmead/bowtie2) v2.3.4.1: doi:10.1038/nmeth.1923\n * [minimap2](https://github.com/lh3/minimap2) v2.17: doi:10.1093/bioinformatics/bty191\n * [hypo](https://github.com/kensung-lab/hypo) v0.1.0: doi:10.1101/2019.12.19.882506\n * [instagraal](https://github.com/koszullab/instaGRAAL) v0.1.6: doi:10.1038/ncomms6695\n * [hicstuff](https://github.com/koszullab/hicstuff) v2.2.2: doi:10.5281/zenodo.2620608\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Facastellanii_hybrid_assembly","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdoret%2Facastellanii_hybrid_assembly","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdoret%2Facastellanii_hybrid_assembly/lists"}