Add sequali

CHANGELOG.md

@@ -23,6 +23,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
 - [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
+- [#134](https://github.com/nf-core/seqinspector/pull/134) Added sequali module.
 
 ### `Fixed`
 

CITATIONS.md

@@ -14,6 +14,10 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [Sequali](https://sequali.readthedocs.io/en/latest/)
+
+> Vorderman R. Sequali: efficient and comprehensive quality control of short- and long-read sequencing data. Bioinformatics Advances, 2025. doi: 10.1093/bioadv/vbaf010
+
 - [SeqFu](https://telatin.github.io/seqfu2/)
 
 > Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059

README.md

@@ -32,7 +32,7 @@
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
-2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [`Sequali`](https://sequali.readthedocs.io/en/latest/))
 3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage

assets/multiqc_config.yml

@@ -13,3 +13,6 @@ report_section_order:
 export_plots: true
 
 disable_version_detection: true
+
+use_filename_as_sample_name:
+  - "sequali"

docs/output.md

@@ -12,6 +12,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
+- [Sequali](#sequali) - Sequence quality metrics for short and long reads
 - [SeqFu Stats](#seqfu_stats) - Statistics for FASTA or FASTQ files
 - [FastQ Screen](#fastqscreen) - Mapping against a set of references for basic contamination QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
@@ -42,6 +43,19 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### Sequali
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `sequali/`
+  - `*.html`: Sequali report containing quality metrics.
+  - `*.jsom`: JSON containing the Sequali data, used for generating MultiQC report.
+
+</details>
+
+[Sequali](https://sequali.readthedocs.io/en/latest/) gives general quality metrics for short and long sequenced reads. It provides information about the quality score distribution across your reads, GC content, duplication levels, length distribution, adapter contamination (Illumina and Oxford Nanopore) and overrepresented sequences.
+
 ### FastQ Screen
 
 <details markdown="1">

modules.json

@@ -40,6 +40,11 @@
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
+                    },
+                    "sequali": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
                     }
                 }
             },