nailpolish summary
Quickly review the quality and duplicate rate of the dataset. The reads must first have been indexed.
Usage
$ nailpolish summary --help
Generate a summary of duplicate statistics from an index file
Usage: nailpolish summary [OPTIONS] <INPUT>
Arguments:
<INPUT> Input .fastq file
Options:
-o, --output <OUTPUT> Output .html file. By default, will write to <file>.summary.html
-h, --help Print help
Output
A brief summary of the dataset is printed to the terminal:
[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
Total read count is every read in the file: those which were indexed under a barcode,
plus those which had no barcode and were skipped. Reads without barcodes are only
possible if the index was built with
--skip-unmatched — without that flag, nailpolish
index errors on the first read it cannot match.
Singleton groups and Duplicate groups split the indexed groups by size: groups with a
single read, and groups with two or more reads (along with the total number of reads in
them). These are the counts before consensus calling — nailpolish
consensus reports them again after false-duplicate detection, which
splits some duplicate groups into smaller groups and singletons.
The full report, including the distribution of duplicate group sizes, is written to the HTML file.