Quick Start

This quick start guide will walk you through installing Nailpolish and running it on a small demo dataset. The demo dataset is a small subset of the scmixology2 Chromium 10x droplet-based dataset, sequenced using Nanopore technology, released by Tian et al. (2021).

Our Flexiplex tool is used to demultiplex the dataset.

Install

For more information, see Install.

For x64 Linux, run:

curl --proto '=https' --tlsv1.2 -LsSf "https://github.com/DavidsonGroup/nailpolish/releases/download/nightly_develop/nailpolish" -o nailpolish
chmod +x nailpolish

Get test files

Download the scmixology2 subset reads using:

wget https://github.com/DavidsonGroup/nailpolish/releases/download/sample-fastq-for-quickstart/scmixology2_sample.fastq

Indexation

For more information, see nailpolish index.

By default, nailpolish expects the barcode and UMI to be in the @BC_UMI format at the start of the header. Alternative barcode and UMI formats can be provided through either a preset (one of bc-umi, umi-tools, illumina) or a custom barcode regex.

# write the index file to `index.tsv`
nailpolish index --index index.tsv scmixology2_sample.fastq

Summary of duplicate count

For more information, see nailpolish summary.

A .html file can be generated to summarise some key statistics about the input reads. The output file is written to summary.html by default.

nailpolish summary index.tsv

Consensus call duplicates

For more information, see nailpolish call.

By consensus calling duplicates, only one read is returned per UMI group. For singleton reads, there is no change (apart from including UMI group information in the header).

nailpolish call \
  --index index.tsv \
  --input scmixology2_sample.fastq \
  --output scmixology2_sample_consensus_called.fastq \
  --threads 4 

There are alternative parameters which can be passed to configure the output. See the nailpolish call documentation for more.