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Merged
cokelaer merged 2 commits into from
Jun 2, 2026
Merged

Add optional FastQC on raw reads (--do-fastqc); bump to 1.5.0 #33

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48832d0
Add optional FastQC on raw reads (--do-fastqc); bump to 1.5.0
cokelaer Jun 1, 2026
44a6852
update doc and container
cokelaer Jun 2, 2026
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9 changes: 6 additions & 3 deletions README.rst
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Expand Up @@ -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
~~~~~
Expand All @@ -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.).

Expand All @@ -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
Expand All @@ -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)
Expand Down Expand Up @@ -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

Expand All @@ -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
Expand Down
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