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add name of ONT repository
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AmstlerStephan committed Mar 6, 2024
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Expand Up @@ -6,7 +6,7 @@ Umi-pipeline-nf

**Umi-pipeline-nf** creates highly accurate single-molecule consensus sequences for unique molecular identifier (UMI)-tagged amplicons from nanopore sequencing data.
The pipeline can be run for the whole fastq_pass folder of your nanopore run and, per default, outputs the aligned consensus sequences of each UMI cluster in bam file. The optional variant calling creates a vcf file for all variants that are found in the consensus sequences.
umi-pipeline-nf orignates from a snakemake-based analysis pipeline ([ONT UMI analysis pipeline](https://github.com/nanoporetech/pipeline-umi-amplicon); originally developed by [Karst et al, Nat Biotechnol 18:165–169, 2021](https://www.nature.com/articles/s41592-020-01041-y)). We migrated the pipeline to [Nextflow](https://www.nextflow.io) and included several optimizations and [additional functionalities](#main-adaptations).
Umi-pipeline-nf orignates from a snakemake-based analysis pipeline ([pipeline-umi-amplicon](https://github.com/nanoporetech/pipeline-umi-amplicon); originally developed by [Karst et al, Nat Biotechnol 18:165–169, 2021](https://www.nature.com/articles/s41592-020-01041-y)). We migrated the pipeline to [Nextflow](https://www.nextflow.io) and included several optimizations and [additional functionalities](#main-adaptations).

![Workflow](docs/images/umi-pipeline-nf_metro-map.svg)

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