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ro-crate-metadata.json
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"description": "[](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml)\n[](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)\n[](https://www.nf-test.com)\n[](https://doi.org/10.5281/zenodo.13748210)\n[](https://www.nextflow.io/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/genomic-medicine-sweden/nallo)\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## Pipeline summary\n\n##### QC\n\n- Read QC with [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino) and [mosdepth](https://github.com/brentp/mosdepth)\n\n##### Alignment & assembly\n\n- Align reads to reference with [minimap2](https://github.com/lh3/minimap2)\n- Assemble genomes with [hifiasm](https://github.com/chhylp123/hifiasm)\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) or [Sniffles](https://github.com/fritzsedlazeck/Sniffles)\n- Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)\n- Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (HiFi only)\n- Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase)\n- Call variants from assembly with [dipcall](https://github.com/lh3/dipcall)\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)\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 [stranger](https://github.com/Clinical-Genomics/stranger)\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\nNIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2\nNIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1\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\nFor 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).\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\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 [`docs/CITATIONS.md`](docs/CITATIONS.md) file.\n",
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