genomic-medicine-sweden / nallo

Introduction **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, nf-core/raredisease, nf-core/nanoseq, PacBio Human WGS Workflow, epi2me-labs/wf-human-variation and brentp/rare-disease-wf. QC • Read QC with FastQC, cramino, mosdepth and peddy Alignment & assembly • Assemble genomes with hifiasm • Align reads and assemblies to reference with minimap2 Variant calling • Call SNVs & joint genotyping with deepvariant and GLNexus • Call SVs with Severus, Sniffles or Sawfish (PacBio only) • Call CNVs with HiFiCNV • Call tandem repeats with TRGT (PacBio only) or STRdust • Call paralogous genes with Paraphase (PacBio only) Phasing and methylation • Phase and haplotag reads with LongPhase, whatshap or HiPhase • Create methylation pileups with modkit or pbcpgtools (PacBio only) • Rare methylation analaysis with methbat profile (PacBio only) Annotation • Annotate SNVs and INDELs with databases of choice, e.g. gnomAD, ClinVar, CADD with echtvar and VEP • Annotate repeat expansions with strdrop and stranger (TRGT only) • Annotate SVs with SVDB and VEP Ranking • Rank SNVs, INDELs, SVs and CNVs with GENMOD Filtering • Filter SNVs, INDELs, SVs and CNVs with filter_vep and bcftools Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with before running the workflow on actual data. Prepare a samplesheet with input data: Supply a reference genome with and choose a matching for your data ( , , ). Now, you can run the pipeline using: However, 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. Credits genomic-medicine-sweden/nallo was originally written by Felix Lenner. We thank the following people for their extensive assistance in the development of this pipeline: Anders Jemt, Annick Renevey, Daniel Schmitz, Lucía Peña-Pérez, Peter Pruisscher, Ramprasad Neethiraj & Alexander Koc. Contributions and Support If you would like to contribute to this pipeline, please see the contributing guidelines. Citations If you use genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: 10.5281/zenodo.13748210. This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license. > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. An extensive list of references for the tools used by the pipeline can be found in the file.