Single-cell/nuclei pipeline for data derived from Oxford Nanopore

Genome assembly workflow for nanopore reads, for TSI

Input:

• Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)

Optional settings to specify when the workflow is run:

• [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
• [2] filtering: min average read quality score. default = 10
• [3] filtering: min read length. default = 200
• [4] ...

Assembly and intrahost/low-frequency variant calling for viral samples

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A pipeline to demultiplex, QC and map Nanopore data

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A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

Simple bacterial assembly and annotation pipeline.

pod5_by_pore

A Snakemake workflow to take the POD5 files produced by an Oxford Nanopore sequencing run and re-batch them by pore (ie. by channel).

This is useful if you want to run duplex basecalling because you can meaningfully run "dorado duplex" on a single (or a subset of) the POD5 files.

Know issues

It is assumed all POD5 input files are from the same sequencing run, but this is not checked.

MoP2- DSL2 version of Master of Pores

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Workflow for LongRead Quality Control and Filtering

• NanoPlot (read quality control) before and after filtering
• Filtlong (read trimming)
• Kraken2 taxonomic read classification before and after filtering
• Minimap2 read filtering based on given references

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows

**How to setup and use an UNLOCK ...

- Deprecated -

See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367

And other workflows: https://workflowhub.eu/projects/16#workflows

Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning

• Workflow Nanopore Quality
• Kraken2 taxonomic classification of FASTQ reads
• Flye (de-novo assembly)
• Medaka (assembly polishing)
• metaQUAST (assembly quality reports)

When Illumina reads are provided:

• Workflow ...