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            "description": "[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/genomic-medicine-sweden/nallo)\n[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)\n[![Cite with Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.13748210.svg)](https://doi.org/10.5281/zenodo.13748210)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/genomic-medicine-sweden/nallo)\n\n<p align=\"center\">\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nallo_dark.png\">\n    <img width=250px alt=\"Nallo logo\" src=\"docs/images/nallo_light.png\">\n  </picture>\n</p>\n\n## Introduction\n\n**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. Heavily influenced by best-practice pipelines such as [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf).\n\n<picture align=\"center\">\n  <img alt=\"genomic-medicine-sweden/nallo workflow\" src=\"docs/images/nallo_metromap.png\">\n</picture>\n\n##### QC\n\n- Read QC with [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino), [mosdepth](https://github.com/brentp/mosdepth) and [peddy](https://github.com/brentp/peddy)\n\n##### Alignment & assembly\n\n- Assemble genomes with [hifiasm](https://github.com/chhylp123/hifiasm)\n- Align reads and assemblies to reference with [minimap2](https://github.com/lh3/minimap2)\n\n##### Variant calling\n\n- Call SNVs & joint genotyping with [deepvariant](https://github.com/google/deepvariant) and [GLNexus](https://github.com/dnanexus-rnd/GLnexus)\n- Call SVs with [Severus](https://github.com/KolmogorovLab/Severus), [Sniffles](https://github.com/fritzsedlazeck/Sniffles) or [Sawfish](https://github.com/PacificBiosciences/sawfish) (PacBio only)\n- Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)\n- Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (PacBio only) or [STRdust](https://github.com/wdecoster/STRdust)\n- Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase) (PacBio only)\n\n##### Phasing and methylation\n\n- Phase and haplotag reads with [LongPhase](https://github.com/twolinin/longphase), [whatshap](https://github.com/whatshap/whatshap) or [HiPhase](https://github.com/PacificBiosciences/HiPhase)\n- Create methylation pileups with [modkit](https://github.com/nanoporetech/modkit) or [pbcpgtools](https://github.com/PacificBiosciences/pb-CpG-tools) (PacBio only)\n- Rare methylation analaysis with [methbat profile](https://github.com/PacificBiosciences/MethBat) (PacBio only)\n\n##### Annotation\n\n- Annotate SNVs and INDELs with databases of choice, e.g. [gnomAD](https://gnomad.broadinstitute.org), [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/), [CADD](https://cadd.gs.washington.edu) with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep)\n- Annotate repeat expansions with [strdrop](https://github.com/dnil/strdrop) and [stranger](https://github.com/Clinical-Genomics/stranger) (TRGT only)\n- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep)\n\n##### Ranking\n\n- Rank SNVs, INDELs, SVs and CNVs with [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n##### Filtering\n\n- Filter SNVs, INDELs, SVs and CNVs with [filter_vep](https://www.ensembl.org/vep) and [bcftools](https://samtools.github.io/bcftools/bcftools.html)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nPrepare a samplesheet with input data:\n\n`samplesheet.csv`\n\n```\nproject,sample,file,family_id,paternal_id,maternal_id,sex,phenotype\n my_project,HG002,/path/to/HG002.fastq.gz,NIST,HG003,HG004,1,2\n my_project,HG003,/path/to/HG003.bam,NIST,0,0,1,1\n my_project,HG004,/path/to/HG004.bam,NIST,0,0,2,1\n```\n\nSupply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline using:\n\n```bash\nnextflow run genomic-medicine-sweden/nallo \\\n    -profile <docker/singularity/.../institute> \\\n    --input samplesheet.csv \\\n    --preset <revio/pacbio/ONT_R10> \\\n    --fasta <reference.fasta> \\\n    --outdir <OUTDIR>\n```\n\nHowever, to run most parts of the pipeline you will need to supply additional reference files. For more details and further functionality, please refer to the [documentation](http://genomic-medicine-sweden.github.io/nallo/).\n\n## Credits\n\ngenomic-medicine-sweden/nallo was originally written by [Felix Lenner](https://github.com/fellen31).\n\nWe thank the following people for their extensive assistance in the development of this pipeline: [Anders Jemt](https://github.com/jemten), [Annick Renevey](https://github.com/rannick), [Daniel Schmitz](https://github.com/Schmytzi), [Luc\u00eda Pe\u00f1a-P\u00e9rez](https://github.com/Lucpen), [Peter Pruisscher](https://github.com/peterpru), [Ramprasad Neethiraj](https://github.com/ramprasadn), [Alexander Koc](https://github.com/alkc) & [Sofia Demmou](https://github.com/sofiademmou).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: [10.5281/zenodo.13748210](https://doi.org/10.5281/zenodo.13748210).\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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\nAn extensive list of references for the tools used by the pipeline can be found in the Software Versions section of the MultiQC report generated with the pipeline.\n",
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}