diff --git a/README.rst b/README.rst
index 2be32d5..41ec3d6 100644
--- a/README.rst
+++ b/README.rst
@@ -29,7 +29,7 @@ If you already have all requirements, you can install the packages using pip::
 
     pip install sequana_mapper --upgrade
 
-You will need third-party software such as fastqc. Please see below for details.
+You will need third-party software such as bwa and samtools. Please see below for details.
 
 Usage
 ~~~~~
@@ -52,7 +52,7 @@ For capture-seq projects (feature counting)::
 This creates a ``mapper/`` directory with the pipeline and configuration file. Execute the pipeline locally::
 
     cd mapper
-    sh mapper.sh
+    bash mapper.sh
 
 See ``.sequana/profile/config.yaml`` to tune Snakemake behaviour (cores, cluster settings, etc.).
 
@@ -70,7 +70,7 @@ Images are downloaded in the working directory but you can store them in a share
 and then::
 
     cd mapper
-    sh mapper.sh
+    bash mapper.sh
 
 
 Requirements
@@ -83,6 +83,7 @@ This pipeline requires the following executables (install via bioconda/conda):
 - **bowtie2** — alternative short-read aligner
 - **samtools** / **sambamba** — BAM processing
 - **bamtools** — BAM statistics
+- **fastqc** — raw-read quality control (optional, ``--do-fastqc``)
 - **deeptools** — bigwig generation (``bamCoverage``)
 - **bedtools** — genome arithmetic
 - **subread** — feature counting (``featureCounts``, capture-seq only)
@@ -117,6 +118,7 @@ filtered BAM files, a MultiQC HTML report, and optionally coverage tracks and fe
 **Optional outputs**:
 
 - ``--do-coverage`` — runs ``sequana_coverage`` for depth-of-coverage analysis (prokaryotes)
+- ``--do-fastqc`` — runs ``fastqc`` on the raw input reads (included in the MultiQC report)
 - ``--create-bigwig`` — generates bigwig files via ``bamCoverage`` (deeptools)
 - ``--capture-annotation-file`` — enables ``featureCounts`` for capture-seq efficiency metrics
 
@@ -135,6 +137,7 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+1.5.0     * add optional FastQC on raw reads (--do-fastqc), included in MultiQC
 1.4.1     * update to use wrappers.shells and wrappers.snippets
             drop wrappers usage
 1.4.0     * update wrappers to v24.8.29
diff --git a/doc/conf.py b/doc/conf.py
index 6c7dbc5..5729e98 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -11,10 +11,12 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import os
+import sys
+
 import sphinx
 
-sys.path.insert(0, os.path.abspath('sphinxext'))
+sys.path.insert(0, os.path.abspath("sphinxext"))
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -24,9 +26,11 @@
 
 # This is for ReadTheDoc
 import matplotlib
-matplotlib.use('Agg')
+
+matplotlib.use("Agg")
 
 import pkg_resources
+
 version = pkg_resources.require(pkg_name)[0].version
 
 import matplotlib
@@ -36,55 +40,56 @@
 author = "Thomas Cokelaer"
 title = "Sequana mapper pipeline"
 copyright = author + ", 2016-2019"
-project = 'Sequana mapper pipeline'
+project = "Sequana mapper pipeline"
 
 import easydev
 from easydev import get_path_sphinx_themes
 
-
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 
 extensions = [
-    'sphinx.ext.autodoc',
-    ('sphinx.ext.imgmath'  # only available for sphinx >= 1.4
-                  if sphinx.version_info[:2] >= (1, 4)
-                  else 'sphinx.ext.pngmath'),
-    'sphinx.ext.coverage',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    (
+        "sphinx.ext.imgmath"  # only available for sphinx >= 1.4
+        if sphinx.version_info[:2] >= (1, 4)
+        else "sphinx.ext.pngmath"
+    ),
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
     "numpydoc.numpydoc",
-    'matplotlib.sphinxext.plot_directive',
-    'sphinx.ext.autosummary',
-    "sequana.sphinxext.snakemakerule"
-    ]
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx.ext.autosummary",
+    "sequana.sphinxext.snakemakerule",
+]
 # note that the numpy directives is buggy. Example: class and init are not recognised as two entities for the autoclass_content=both here below
 
 math_number_all = False
 
-todo_include_todos=True
+todo_include_todos = True
 jscopybutton_path = "copybutton.js"
-autoclass_content = 'both'
+autoclass_content = "both"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
 project = project
@@ -95,34 +100,34 @@
 # built documents.
 #
 # The short X.Y version.
-version = 'Current version: ' + str(version) 
+version = "Current version: " + str(version)
 # The full version, including alpha/beta/rc tags.
 release = release
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
-#unused_docs = []
+# unused_docs = []
 
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_trees = ['_build']
+exclude_trees = ["_build"]
 exclude_patterns = []
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
@@ -133,7 +138,7 @@
 show_authors = True
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 modindex_common_prefix = ["sequana."]
@@ -150,22 +155,17 @@
 def touch_example_backreferences(app, what, name, obj, options, lines):
     # generate empty examples files, so that we don't get
     # inclusion errors if there are no examples for a class / module
-    examples_path = os.path.join(app.srcdir, "modules", "generated",
-                                 "%s.examples" % name)
+    examples_path = os.path.join(app.srcdir, "modules", "generated", "%s.examples" % name)
     if not os.path.exists(examples_path):
         # touch file
-        open(examples_path, 'w').close()
-
+        open(examples_path, "w").close()
 
 
 # Add the 'copybutton' javascript, to hide/show the prompt in code
 # examples
 def setup(app):
-    app.add_javascript('copybutton.js')
-    app.connect('autodoc-process-docstring', touch_example_backreferences)
-
-
-
+    app.add_javascript("copybutton.js")
+    app.connect("autodoc-process-docstring", touch_example_backreferences)
 
 
 # -- Options for HTML output ---------------------------------------------------
@@ -175,7 +175,8 @@ def setup(app):
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"
 if not on_rtd:
     import sphinx_rtd_theme
-    html_theme = 'sphinx_rtd_theme'
+
+    html_theme = "sphinx_rtd_theme"
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 else:
     html_theme = "default"
@@ -184,53 +185,52 @@ def setup(app):
 # further.  For a list of options available for each theme, see the
 # documentation.
 # the user theme contains the otpions 'homepage', which is populated here
-#html_theme_options = {'homepage': init_sphinx.url}
+# html_theme_options = {'homepage': init_sphinx.url}
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = [get_path_sphinx_themes()]
-
+# html_theme_path = [get_path_sphinx_themes()]
 
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 html_short_title = "sequana"
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = "../../share/data/images/crx_logo.png"
+# html_logo = "../../share/data/images/crx_logo.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = "../../share/data/images/crx_logo.ico"
+# html_favicon = "../../share/data/images/crx_logo.ico"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = "%b %d, %Y"
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_index = 'index.html'
+html_index = "index.html"
 
-#Custom sidebar templates, maps page names to templates.
-#html_sidebars = {
-#                    'index': [ 'indexsidebar.html'], 
+# Custom sidebar templates, maps page names to templates.
+# html_sidebars = {
+#                    'index': [ 'indexsidebar.html'],
 #                    'contents':'indexsidebar.html',
-#}
+# }
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {   'index': 'index.html'}
+# html_additional_pages = {   'index': 'index.html'}
 
 
 # If false, no module index is generated.
@@ -250,18 +250,18 @@ def setup(app):
 html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'doc'
+htmlhelp_basename = "doc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -270,52 +270,48 @@ def setup(app):
 pngmath_use_preview = True
 
 # The font size ('10pt', '11pt' or '12pt').
-latex_font_size = '10pt'
+latex_font_size = "10pt"
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'main.tex', title,
-   author, 'manual'),
+    ("index", "main.tex", title, author, "manual"),
 ]
 
-latex_elements = { 'inputenc': '\\usepackage[utf8]{inputenc}' }
+latex_elements = {"inputenc": "\\usepackage[utf8]{inputenc}"}
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
 latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Additional stuff for the LaTeX preamble.
 
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output --------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', project, project,
-     [author], 1)
-]
+man_pages = [("index", project, project, [author], 1)]
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "python": ('http://docs.python.org/', None),
+    "python": ("http://docs.python.org/", None),
 }
diff --git a/doc/index.rst b/doc/index.rst
index 675d27e..13fb184 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -36,6 +36,3 @@ What is Sequana ?
 To join the project, please let us know on `github <https://github.com/sequana/sequana/issues/306>`_.
 
 For more information, please see `github <https://sequana.readthedocs.io>`_.
-
-
-
diff --git a/environment.yml b/environment.yml
index 3489b98..76e2120 100644
--- a/environment.yml
+++ b/environment.yml
@@ -11,6 +11,7 @@ dependencies:
 - deeptools
 - bedtools
 - bamtools
+- fastqc
 - mosdepth
 - sambamba
 - subread
diff --git a/pyproject.toml b/pyproject.toml
index 6ac41ab..fdd3576 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-mapper"
-version = "1.4.1"
+version = "1.5.0"
 description = "A multi-sample mapper to map reads onto a reference"
 authors = ["Sequana Team"]
 license = "BSD-3"
diff --git a/sequana_pipelines/mapper/__init__.py b/sequana_pipelines/mapper/__init__.py
index 71b8c2e..1746818 100644
--- a/sequana_pipelines/mapper/__init__.py
+++ b/sequana_pipelines/mapper/__init__.py
@@ -1,5 +1,6 @@
 import importlib.metadata as metadata
 
+
 def get_package_version(package_name):
     try:
         version = metadata.version(package_name)
@@ -7,4 +8,5 @@ def get_package_version(package_name):
     except metadata.PackageNotFoundError:
         return f"{package_name} not found"
 
+
 version = get_package_version("sequana-mapper")
diff --git a/sequana_pipelines/mapper/config.yaml b/sequana_pipelines/mapper/config.yaml
index c26571f..d28e0b2 100644
--- a/sequana_pipelines/mapper/config.yaml
+++ b/sequana_pipelines/mapper/config.yaml
@@ -21,16 +21,17 @@ general:
 
 apptainers:
     bamtools: https://zenodo.org/record/10211475/files/bamtools_2.5.2.img
-    bowtie2: https://zenodo.org/record/8037162/files/sequana_minimal_23.6.13.img
+    bowtie2: https://zenodo.org/record/19127803/files/sequana_minimal_26.3.19.img 
     bwa: https://zenodo.org/record/8037162/files/sequana_minimal_23.6.13.img
-    deeptools: https://zenodo.org/record/18257162/files/sequana_tools_26.1.14.img
+    deeptools: https://zenodo.org/record/19187268/files/deeptools_3.5.6.img 
+    fastqc: https://zenodo.org/record/7015004/files/fastqc_0.11.9-py3.img
     graphviz: https://zenodo.org/record/7928262/files/graphviz_7.0.5.img
-    minimap2: https://zenodo.org/record/18257162/files/sequana_tools_26.1.14.img
+    minimap2: https://zenodo.org/record/19127803/files/sequana_minimal_26.3.19.img 
     multiqc: https://zenodo.org/record/10205070/files/multiqc_1.16.0.img
     samtools: https://zenodo.org/record/7437898/files/samtools_1.16.1.img
-    sequana_coverage:  https://zenodo.org/record/13946414/files/sequana_coverage_0.18.0.img
+    sequana_coverage:  https://zenodo.org/record/20467327/files/sequana_0.22.0.img 
     seqkit: https://zenodo.org/record/7821924/files/seqkit_2.4.0.img
-    subread: https://zenodo.org/record/18257162/files/sequana_tools_26.1.14.img
+    subread: https://zenodo.org/record/8037099/files/subread_2.0.3.img
     mosdepth: https://zenodo.org/record/12805460/files/mosdepth_0.3.8.img
 
 
@@ -161,6 +162,21 @@ sequana_coverage:
         mem: 8G
 
 
+#############################################################################
+##   FastQC computes quality-control metrics on the raw input FastQ files.
+##
+## :Parameters:
+##
+## - do: set to true to run FastQC on the raw reads
+## - options: any options recognised by fastqc (e.g. --nogroup)
+fastqc:
+    do: false
+    options: --nogroup
+    threads: 4
+    resources:
+        mem: 4G
+
+
 #############################################################################
 ##   MultiQC aggregates results from bioinformatics analyses across many
 ##   samples into a single report.
diff --git a/sequana_pipelines/mapper/main.py b/sequana_pipelines/mapper/main.py
index adce2d8..e02627f 100755
--- a/sequana_pipelines/mapper/main.py
+++ b/sequana_pipelines/mapper/main.py
@@ -32,6 +32,7 @@
             "--capture-annotation-file",
             "--create-bigwig",
             "--do-coverage",
+            "--do-fastqc",
             "--nanopore",
             "--pacbio",
             "--reference-file",
@@ -57,6 +58,7 @@
 @click.option("--reference-file", required=True, help="You input reference file in fasta format")
 @click.option("--annotation-file", help="Used by the sequana_coverage tool if provided")
 @click.option("--do-coverage", is_flag=True, help="Use sequana_coverage (prokaryotes)")
+@click.option("--do-fastqc", is_flag=True, help="Run FastQC on the raw input reads (included in MultiQC report)")
 @click.option(
     "--pacbio",
     is_flag=True,
@@ -99,6 +101,9 @@ def main(**options):
     if options.do_coverage:
         cfg.sequana_coverage.do = True
 
+    if options.do_fastqc:
+        cfg.fastqc.do = True
+
     if options.create_bigwig:
         cfg.general.create_bigwig = True
 
diff --git a/sequana_pipelines/mapper/mapper.rules b/sequana_pipelines/mapper/mapper.rules
index cf9d2ef..20e1127 100644
--- a/sequana_pipelines/mapper/mapper.rules
+++ b/sequana_pipelines/mapper/mapper.rules
@@ -28,6 +28,8 @@ manager = PipelineManager("mapper", config)
 def get_multiqc_inputs():
     inputs = []
     inputs += expand("{sample}/bamtools_stats/sequana_bamtools_stats_{sample}.txt", sample=manager.samples)
+    if config["fastqc"]["do"]:
+        inputs += expand("{sample}/fastqc/fastqc.done", sample=manager.samples)
     if config["feature_counts"]["do"]:
         inputs += expand("{sample}/feature_counts/{sample}_feature.out", sample=manager.samples)
     if config["sequana_coverage"]["do"]:
@@ -87,6 +89,8 @@ if config['general']['mapper'] == "bwa":
             fai="reference/genome.fasta.fai",
             reference="reference/genome.fasta"
         output:
+            sam=temp("{sample}/{sample}.sam"),
+            bam=temp("{sample}/{sample}.bam"),
             sorted="{sample}/{sample}.sorted.bam"
         log:
             "{sample}/bwa/{sample}.log"
@@ -99,7 +103,7 @@ if config['general']['mapper'] == "bwa":
         container:
             config['apptainers']['bwa']
         shell:
-            manager.get_shell("bwa/align", "v1")
+            manager.get_shell("bwa/align", "v2")
 
 elif config['general']['mapper'] == 'bwa_split':
 
@@ -115,23 +119,36 @@ elif config['general']['mapper'] == 'bwa_split':
             seqkit split2 --by-size {params.nreads} -O {wildcards.sample}/split -1 {input[0]} -2 {input[1]}
             """
 
-    def get_bwa_input():
+    def _seqkit_stem(filename):
+        # seqkit split2 names parts <stem>.part_NNN.fastq.gz where <stem> is
+        # the input basename minus the fastq/fq[.gz] extension. Derive it from
+        # the real raw filenames so we do not assume a fixed readtag suffix.
+        base = os.path.basename(filename)
+        for ext in (".fastq.gz", ".fq.gz", ".fastq", ".fq"):
+            if base.endswith(ext):
+                return base[: -len(ext)]
+        return base
+
+    def get_bwa_input(wildcards):
+        files = manager.samples[wildcards.sample]
         if manager.paired is True:
             return (
-                    "{sample}/split/{sample}_R1_001.{splitid}.fastq.gz",
-                    "{sample}/split/{sample}_R2_001.{splitid}.fastq.gz"
+                    f"{wildcards.sample}/split/{_seqkit_stem(files[0])}.{wildcards.splitid}.fastq.gz",
+                    f"{wildcards.sample}/split/{_seqkit_stem(files[1])}.{wildcards.splitid}.fastq.gz"
                     )
         else:
-            return "{sample}/split/{sample}_R1_001.{splitid}.fastq.gz"
+            return f"{wildcards.sample}/split/{_seqkit_stem(files[0])}.{wildcards.splitid}.fastq.gz"
 
     # intermediate
     rule bwa_intermediate:
         input:
-            fastq=get_bwa_input(),
+            fastq=get_bwa_input,
             bwa_bwt="reference/genome.fasta.bwt",
             fai="reference/genome.fasta.fai",
             reference="reference/genome.fasta"
         output:
+            sam=temp("{sample}/split/{sample}.{splitid}.sam"),
+            bam=temp("{sample}/split/{sample}.{splitid}.bam"),
             sorted=temp("{sample}/split/{sample}.sorted.{splitid}.bam")
         log:
             "{sample}/split/{sample}.{splitid}.log"
@@ -144,7 +161,7 @@ elif config['general']['mapper'] == 'bwa_split':
         container:
             config['apptainers']['bwa']
         shell:
-            manager.get_shell("bwa/align", "v1")
+            manager.get_shell("bwa/align", "v2")
 
     def aggregate_bwa(wildcards):
         checkpoint_output = checkpoints.split_fasta.get(**wildcards).output[0]
@@ -256,6 +273,27 @@ rule filtering_bam:
         """
 
 
+if config["fastqc"]["do"]:
+    rule fastqc:
+        input:
+            manager.getrawdata()
+        output:
+            done="{sample}/fastqc/fastqc.done"
+        params:
+            options=config["fastqc"]["options"],
+            working_directory="{sample}/fastqc/"
+        threads:
+            config["fastqc"]["threads"]
+        log:
+            "{sample}/fastqc/fastqc.log"
+        resources:
+            **config["fastqc"]["resources"]
+        container:
+            config['apptainers']['fastqc']
+        shell:
+            manager.get_shell("fastqc/run", "v1")
+
+
 # sample should be included at the end of the filename for the multiqc to work
 rule bamtools_stats:
     input:
@@ -379,7 +417,7 @@ rule multiqc:
         options=config['multiqc']['options'],
         input_directory=config['multiqc']['input_directory'],
         config_file=config['multiqc']['config_file'],
-        modules=config['multiqc']['modules']
+        modules=config['multiqc']['modules'] + (" fastqc" if config["fastqc"]["do"] else "")
     log:
         "multiqc/multiqc.log"
     resources:
diff --git a/sequana_pipelines/mapper/schema.yaml b/sequana_pipelines/mapper/schema.yaml
index f56cc04..c2ca184 100644
--- a/sequana_pipelines/mapper/schema.yaml
+++ b/sequana_pipelines/mapper/schema.yaml
@@ -64,6 +64,23 @@ mapping:
                      "mem":
                         type: str
 
+    "fastqc":
+        type: map
+        mapping:
+            "do":
+                type: bool
+                default: False
+            "options":
+                type: str
+            "threads":
+                type: int
+                range: { min: 1 }
+            "resources":
+                 type: map
+                 mapping:
+                     "mem":
+                        type: str
+
     "multiqc":
         type: map
         mapping:
diff --git a/sequana_pipelines/mapper/tools.txt b/sequana_pipelines/mapper/tools.txt
index a22c1d9..33864cb 100644
--- a/sequana_pipelines/mapper/tools.txt
+++ b/sequana_pipelines/mapper/tools.txt
@@ -3,6 +3,7 @@ bedtools
 bowtie2
 bwa
 deeptools
+fastqc
 featureCounts
 minimap2
 sambamba
diff --git a/test/test_main.py b/test/test_main.py
index e8a2e06..ea8db2d 100644
--- a/test/test_main.py
+++ b/test/test_main.py
@@ -1,3 +1,4 @@
+import glob
 import os
 import subprocess
 import sys
@@ -79,6 +80,25 @@ def test_standalone_script_saf(tmpdir):
         assert results.exit_code == 0
 
 
+def test_standalone_script_fastqc(tmpdir):
+    with tempfile.TemporaryDirectory() as directory:
+        runner = CliRunner()
+        results = runner.invoke(
+            main,
+            [
+                "--input-directory",
+                sharedir,
+                "--reference-file",
+                sharedir + "/measles.fa",
+                "--working-directory",
+                directory,
+                "--force",
+                "--do-fastqc",
+            ],
+        )
+        assert results.exit_code == 0
+
+
 def test_full():
 
     with tempfile.TemporaryDirectory() as directory:
@@ -86,7 +106,7 @@ def test_full():
         wk = directory
 
         cmd = "sequana_mapper --input-directory {} "
-        cmd += " --working-directory {}  --force "
+        cmd += " --working-directory {}  --force --do-fastqc "
         cmd += " --reference-file " + sharedir + "/measles.fa"
         cmd = cmd.format(sharedir, wk)
         subprocess.call(cmd.split())
@@ -95,6 +115,11 @@ def test_full():
 
         assert os.path.exists(wk + "/multiqc/multiqc_report.html")
 
+        # --do-fastqc must produce per-sample FastQC output
+        fastqc_done = glob.glob(wk + "/*/fastqc/fastqc.done")
+        assert len(fastqc_done) > 0
+        assert len(glob.glob(wk + "/*/fastqc/*_fastqc.zip")) > 0
+
 
 def test_version():
     cmd = "sequana_mapper --version"