+ "description": "# nf-core/nfmicrofinder\n\n[](https://github.com/nf-core/nfmicrofinder/actions/workflows/ci.yml)\n[](https://github.com/nf-core/nfmicrofinder/actions/workflows/linting.yml)[](https://nf-co.re/nfmicrofinder/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/nfmicrofinder)\n\n[](https://nfcore.slack.com/channels/nfmicrofinder)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/nfmicrofinder** is a bioinformatics pipeline that aids in the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to the start of the genome assembly FASTA file.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), 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](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.\n\n## Pipeline Summary\n\n1. Input validation and parameter checks\n2. Index reference genome using Miniprot\n3. Align protein sequences to genome using Miniprot\n4. Filter alignments based on quality thresholds (identity \u226570%, score \u226560)\n5. Sort FASTA file based on filtered alignments to prioritize microchromosomes\n6. Generate final reordered assembly and pipeline reports\n\n## Quick Start\n\n1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=24.10.5`)\n\n2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_\n\n3. Download the pipeline and test it on a minimal dataset with a single command:\n\n ```bash\n nextflow run main.nf -profile test,docker\n ```\n\n > Note that it is recommend to use the `-profile` parameter to specify the container technology of your choice. See the [nf-core pipeline documentation](https://nf-co.re/usage/running#software-dependencies) for more information.\n\n4. Start running your own analysis!\n\n ```bash\n nextflow run main.nf \\\n --input genome.fa \\\n --pep_file proteins.fa \\\n --output_prefix my_analysis \\\n --outdir <OUTDIR>\n ```\n\n## Documentation\n\nThe nfmicrofinder pipeline comes with documentation about the pipeline [usage](docs/usage.md) and [output](docs/output.md).\n\n## Credits\n\nnfmicrofinder was originally written by Yumi Sims and Will Eagle ([@weaglesBio](https://github.com/weaglesBio)).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Jim Downie ([@prototaxites](https://github.com/prototaxites))\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
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