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 -LsSf "https://github.com/DavidsonGroup/nailpolish/releases/download/latest/nailpolish" -o nailpolish
chmod +x nailpolish
Download the example scmixology2_sample dataset 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.
$ nailpolish index scmixology2_sample.fastq
[16:17:08] nailpolish v0.2.2, commit #65a177c-modified
[16:17:08] CMD: ../target/release/nailpolish index scmixology2_sample.fastq
[16:17:08] Indexing 28.9MB from scmixology2_sample.fastq
[16:17:08]
[16:17:08] bytes %
[16:17:08] 28.9MB 100.0%
[16:17:08]
[16:17:08] Statistics:
[16:17:08] 14,143 reads in total
[16:17:08] 14,143 reads with barcodes
[16:17:08] 0 reads without barcodes
[16:17:08] completed in 0.0s runtime
[16:17:08] Writing to scmixology2_sample.fastq.nailpolish.idx...
[16:17:08] real time: 0 sec; CPU: 0 sec; peak RSS: 10.984 MB
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 will be written to scmixology2_sample.summary.html.
$ nailpolish summary scmixology2_sample.fastq
[16:17:49] nailpolish v0.2.2, commit #65a177c-modified
[16:17:49] CMD: ../target/release/nailpolish summary scmixology2_sample.fastq
[16:17:49] Summarising scmixology2_sample.fastq → scmixology2_sample.summary.html
[16:17:49] Summary written to scmixology2_sample.summary.html. In brief:
[16:17:49] Nailpolish version: nailpolish v0.2.2, commit #65a177c-modified
[16:17:49] File path: scmixology2_sample.fastq
[16:17:49] Dataset size: 28.9 MB
[16:17:49] Index date: 2026-08-13T16:17:08.927358+10:00
[16:17:49] Total read count: 14,143
[16:17:49] Reads with barcodes: 14,143
[16:17:49] Reads without barcodes: 0
[16:17:49] Singleton groups: 10,855
[16:17:49] Duplicate groups: 1,310 (3,288 reads)
[16:17:49] Average quality: 21.2
[16:17:49] Average length: 1030.6
Here is an example summary output file. Open in a new tab...
Consensus call duplicates
For more information, see nailpolish consensus.
$ nailpolish consensus scmixology2_sample.fastq \
-o scmixology2_consensus.fastq \
--threads 4
[16:22:21] nailpolish v0.2.2, commit #65a177c-modified
[16:22:21] CMD: ../target/release/nailpolish consensus scmixology2_sample.fastq -o scmixology2_consensus.fastq --threads 4
[16:22:21] Consensus calling scmixology2_sample.fastq → scmixology2_consensus.fastq
[16:22:21] Using thread pool with 4 threads
[16:22:21] Calling consensus on 0 reads across 12,164 groups
[16:22:21]
[16:22:21] ┌── input groups ───┐ ┌─ false duplicates ─┐
[16:22:21] reads % singleton duplicate detections avg/group filtered
[16:22:25] 14,143 100.0% 10,855 1,310 150 0.11 1
[16:22:25]
[16:22:25] Complete. Final counts, after false-duplicate detection:
[16:22:25] input reads 14143
[16:22:25] singleton groups 11063
[16:22:25] duplicate groups 1252 (3079 reads)
[16:22:25] filtered reads 1
[16:22:25] real time: 3 sec; CPU: 13 sec; peak RSS: 1.219 GB
There are alternative parameters which can be passed to configure the output. See the nailpolish consensus documentation for more.