nf-core · maxulysse · Apr 14, 2026 · Oct 22, 2025 · Oct 23, 2025 · Oct 23, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#109](https://github.com/nf-core/seqinspector/pull/109) Adds ToulligQC module for long read QC
+- [#134](https://github.com/nf-core/seqinspector/pull/134) Added sequali module.
 - [#202](https://github.com/nf-core/seqinspector/pull/202) Added support for fasta fai file as input (via params or igenomes) for the pipeline
 - [#204](https://github.com/nf-core/seqinspector/pull/204) Added Fastp module
 - [#206](https://github.com/nf-core/seqinspector/pull/206) Added FASTQE for more comprehensive QC of FASTQ files

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -58,6 +58,10 @@
 
 - [Seqtk](https://github.com/lh3/seqtk)
 
+- [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
+
 - [ToulligQC](https://github.com/GenomiqueENS/toulligQ)
 
 ## Software packaging/containerisation tools

diff --git a/README.md b/README.md
@@ -42,7 +42,8 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | `QC`                       | [`FASTQE`](https://fastqe.com/)                                                                                     | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `QC`                       | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `QC`                       | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                   | yes          |
-| `Taxonomic Classification` | [`Kraken2`](https://ccb.jhu.edu/software/kraken2/)                                                                  | Performs taxonomic classification and/or profiling                                            | [RNA, DNA]              | No                                                                                      |
+| `QC`                       | [`Sequali`](https://sequali.readthedocs.io/en/latest/)                                                              | Read QC for long and short reads.                                                             | [RNA, DNA]              | [N/A]                                                                                   | yes          |
+| `Taxonomic Classification` | [`Kraken2`](https://ccb.jhu.edu/software/kraken2/)                                                                  | Performs taxonomic classification and/or profiling                                            | [RNA, DNA]              | [N/A]                                                                                   | no           |
 | `QC`                       | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                         | yes          |
 | `QC`                       | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |
 | `Reporting`                | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                   | yes          |
@@ -75,6 +76,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | samtools    | 1.23    |
 | seqfu       | 1.22.3  |
 | seqtk       | 1.4     |
+| sequali     | 0.12.0  |
 
 ## Usage
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -19,6 +19,7 @@ disable_version_detection: true
 
 fn_clean_trim:
   - "_screen" # Added by FastqScreen
+  - ".json"
 
 # Make sample name with indexes a bit prettier
 # for SE: "SampleName_01" -> "SampleName #01"
@@ -35,3 +36,6 @@ table_sample_merge:
   "Read2":
     - type: regex
       pattern: "_2$"
+
+use_filename_as_sample_name:
+  - "sequali"
diff --git a/docs/output.md b/docs/output.md
@@ -20,6 +20,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat
 - [SeqFu](#seqfu) - Statistics for FASTA or FASTQ files
 - [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
 - [FASTQE](#fastqe) - Raw read QC
 - [FastP](#fastp) - Trimming and filtering of raw reads
 - [FastQ Screen](#fastq-screen) - Mapping against a set of references for basic contamination QC
@@ -145,6 +146,19 @@ In this pipeline, the `seqfu stats` module is used to produce general quality me
 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>
+
+- `reports/sequali/[sample_id]/`
+  - `*.html`: Sequali report containing quality metrics.
+  - `*.json`: 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.
+
 ### FASTQE
 
 <details markdown="1">

diff --git a/docs/usage.md b/docs/usage.md
@@ -138,6 +138,7 @@ Currently, the following tools are run as default:
 - picard_collectmultiplemetrics
 - rundirparser
 - seqfu_stats
+- sequali
 
 #### Choose specific tools
 

diff --git a/modules.json b/modules.json
@@ -116,6 +116,12 @@
                         "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33",
                         "installed_by": ["modules"]
                     },
+                    "sequali": {
+                        "branch": "master",
+                        "git_sha": "f37e31e7af4c75dc51c5def63afa521caa941cd6",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/sequali/sequali.diff"
+                    },
                     "toulligqc": {
                         "branch": "master",
                         "git_sha": "d9137377f4dd6246242829772eb1949b96de1ef0",

diff --git a/modules/nf-core/sequali/environment.yml b/modules/nf-core/sequali/environment.yml
diff --git a/modules/nf-core/sequali/main.nf b/modules/nf-core/sequali/main.nf
diff --git a/modules/nf-core/sequali/meta.yml b/modules/nf-core/sequali/meta.yml
diff --git a/modules/nf-core/sequali/sequali.diff b/modules/nf-core/sequali/sequali.diff
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to run",
-                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|toulligqc)?,?)*(?<!,)$",
+                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|sequali|toulligqc)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-sort-amount-asc"
                 },
                 "tools_bundle": {
@@ -64,7 +64,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip - overrides any other means of tools selection",
-                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|toulligqc)?,?)*(?<!,)$",
+                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|multiqcsav|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|sequali|toulligqc)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-window-close "
                 }
             }

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -252,6 +252,7 @@ def toolCitationText() {
         "SAMTOOLS (Danecek et al. 2021),",
         params.sample_size > 0 ? "Seqtk (Li 2021)," : "",
         "SeqFu (Telatin et al. 2021),",
+        "Sequali (Vorderman 2025),",
         ".",
     ].join(' ').trim()
 
@@ -268,6 +269,7 @@ def toolBibliographyText() {
         "<li>Danecek P., Bonfield JK., Liddle J., & al. (2021). Twelve years of SAMtools and BCFtools.</li>",
         params.sample_size > 0 ? "<li>Li, H. SeqTk. Available online: https://github.com/lh3/seqtk (accessed on 6 May 2021)</li>" : "",
         "<li>Telatin, A.; Fariselli, P.; Birolo, G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059</li>",
+        "<li>Vorderman, R. Sequali: efficient and comprehensive quality control of short- and long-read sequencing data. Bioinformatics Advances, 2025. doi: 10.1093/bioadv/vbaf010</li>"
     ].join(' ').trim()
 
     return reference_text
@@ -334,6 +336,7 @@ def defineToolsList(input_bundle, input_tools, input_skip) {
         tools_list << 'picard_collectmultiplemetrics'
         tools_list << 'rundirparser'
         tools_list << 'seqfu_stats'
+        tools_list << 'sequali'
         tools_list << 'toulligqc'
     }
     if ('bam' in bundle_list) {
@@ -352,6 +355,7 @@ def defineToolsList(input_bundle, input_tools, input_skip) {
         tools_list << 'picard_collectmultiplemetrics'
         tools_list << 'rundirparser'
         tools_list << 'seqfu_stats'
+        tools_list << 'sequali'
     }
     if ('illumina' in bundle_list) {
         tools_list << 'checkqc'
@@ -369,6 +373,7 @@ def defineToolsList(input_bundle, input_tools, input_skip) {
         tools_list << 'fastqc'
         tools_list << 'fastqscreen'
         tools_list << 'seqfu_stats'
+        tools_list << 'sequali'
         tools_list << 'toulligqc'
     }
 

diff --git a/tests/.nftignore b/tests/.nftignore
@@ -24,4 +24,5 @@ reports/picard_collectmultiplemetrics/*/alignment_summary_metrics
 reports/picard_collectmultiplemetrics/*/base_distribution_by_cycle_metrics
 reports/picard_collectmultiplemetrics/*/quality_by_cycle_metrics
 reports/picard_collectmultiplemetrics/*/quality_distribution_metrics
+reports/sequali/**
 reports/toulligqc/**