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 (pipeline-umi-amplicon; originally developed by Karst et al, Nat Biotechnol 18:165–169, 2021). We migrated the pipeline to Nextflow and included several optimizations and additional functionalities.
See the output documentation for a detailed overview of the pipeline and its output files.
See the usage documentation for all of the available parameters of the pipeline.
Install nextflow
.
Download the pipeline and test it on a minimal dataset with a single command.
nextflow run genepi/umi-pipeline-nf -r v0.2.1 -profile test,docker
nextflow run genepi/umi-pipeline-nf -r v0.2.1 -c <custom.config> -profile custom,<docker,singularity>
If you use the pipeline please cite our Paper:
Amstler S, Streiter G, Pfurtscheller C, Forer L, Di Maio S, Weissensteiner H, Paulweber B, Schoenherr S, Kronenberg F, Coassin S. Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex Lipoprotein(a) KIV-2 VNTR. bioRxiv. 2024. doi: 10.1101/2024.03.01.582741.
The pipeline was written by (@StephanAmstler).
Nextflow template pipeline: EcSeq.
Snakemake-based ONT pipeline for UMI nanopore sequencing analysis: nanoporetech/pipeline-umi-amplicon.
UMI-corrected nanopore sequencing analysis first shown by: SorenKarst/longread_umi.