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========
Sequali
========
.. introduction start
Sequence quality metrics for FASTQ and uBAM files.
Features:
+ `MultiQC <https://multiqc.info>`_ support since MultiQC version 1.22.
+ Low memory footprint, small install size and fast execution times.
+ Informative graphs that allow for judging the quality of a sequence at
a quick glance.
+ Overrepresentation analysis using 21 bp sequence fragments. Overrepresented
sequences are checked against the NCBI univec database.
+ Estimate duplication rate using a `fingerprint subsampling technique which is
also used in filesystem duplication estimation
<https://www.usenix.org/system/files/conference/atc13/atc13-xie.pdf>`_.
+ Checks for 6 illumina adapter sequences and 17 nanopore adapter sequences
for single read data.
+ Determines adapters by overlap analysis for paired read data.
+ Insert size metrics for paired read data.
+ Per tile quality plots for illumina reads.
+ Channel and other plots for nanopore reads.
+ FASTQ and unaligned BAM are supported. See "Supported formats".
Example reports:
+ `GM24385_1.fastq.gz <https://sequali.readthedocs.io/en/latest/GM24385_1.fastq.gz.html>`_;
HG002 (Genome In A Bottle) on ultra-long Nanopore Sequencing. `Sequence file download <https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/GM24385_1.fastq.gz>`_.
+ `GM24385_1_cut.fastq.gz <https://sequali.readthedocs.io/en/latest/GM24385_1_cut.fastq.gz.html>`_;
``GM24385_1.fastq.gz`` processed with cutadapt:
``cutadapt -o GM24385_1_cut.fastq.gz --cut -64 --cut 64 --minimum-length 500 -Z --max-aer 0.1 GM24385_1.fastq.gz``.
The resulting file has 64 bp cut off from both its ends and after that
filtered for a minimum length of 500 and a maximum average error rate of 0.1.
+ `21C125_R1.fastq.gz <https://sequali.readthedocs.io/en/latest/21C125_R1.fastq.gz.html>`_;
Illumina NovaSeq X paired-end sequencing of *Campylobacter jejuni*. ENA accession:
`ERR11204024 <https://www.ebi.ac.uk/ena/browser/view/ERR11204024>`_.
.. introduction end
For more information check `the documentation <https://sequali.readthedocs.io>`_.
Supported formats
=================
.. formats start
- FASTQ. Only the Sanger variation with a phred offset of 33 and the error rate
calculation of 10 ^ (-phred/10) is supported. All sequencers use this
format today.
- Paired end sequencing data is supported.
- For sequences called by illumina base callers an additional plot with the
per tile quality will be provided.
- For sequences called by guppy additional plots for nanopore specific
data will be provided.
- unaligned BAM. Any alignment flags are currently ignored.
- For uBAM data as delivered by dorado additional nanopore plots will be
provided.
.. formats end
Installation
============
.. installation start
Installation via pip is available with::
pip install sequali
Sequali is also distributed via bioconda. It can be installed with::
conda install -c conda-forge -c bioconda sequali
.. installation end
Quickstart
==========
.. quickstart start
.. code-block::
sequali path/to/my.fastq.gz
This will create a report ``my.fastq.gz.html`` and a json ``my.fastq.gz.json``
in the current working directory.
.. quickstart end
For all command line options checkout the
`usage documentation <https://sequali.readthedocs.io/#usage>`_.
For more extensive information about the module options check the
`documentation on the module options
<https://sequali.readthedocs.io/#module-option-explanations>`_.
Acknowledgements
================
.. acknowledgements start
+ `FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_ for
its excellent selection of relevant metrics. For this reason these metrics
are also gathered by Sequali.
+ The matplotlib team for their excellent work on colormaps. Their work was
an inspiration for how to present the data and their RdBu colormap is used
to represent quality score data. Check their `writings on colormaps
<https://matplotlib.org/stable/users/explain/colors/colormaps.html>`_ for
a good introduction.
+ Wouter de Coster for his `excellent post on how to correctly average phred
scores <https://gigabaseorgigabyte.wordpress.com/2017/06/26/averaging-basecall-quality-scores-the-right-way/>`_.
+ Marcel Martin for providing very extensive feedback.
.. acknowledgements end
License
=======
.. license start
This project is licensed under the GNU Affero General Public License v3. Mainly
to avoid commercial parties from using it without notifying the users that they
can run it themselves. If you want to include code from Sequali in your
open source project, but it is not compatible with the AGPL, please contact me
and we can discuss a separate license.
.. license end
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"description": ".. |python-version-shield| image:: https://img.shields.io/pypi/v/sequali.svg\n :target: https://pypi.org/project/sequali/\n :alt:\n\n.. |conda-version-shield| image:: https://img.shields.io/conda/v/bioconda/sequali.svg\n :target: https://bioconda.github.io/recipes/sequali/README.html\n :alt:\n\n.. |python-install-version-shield| image:: https://img.shields.io/pypi/pyversions/sequali.svg\n :target: https://pypi.org/project/sequali/\n :alt:\n\n.. |license-shield| image:: https://img.shields.io/pypi/l/sequali.svg\n :target: https://github.com/rhpvorderman/sequali/blob/main/LICENSE\n :alt:\n\n.. |docs-shield| image:: https://readthedocs.org/projects/sequali/badge/?version=latest\n :target: https://sequali.readthedocs.io/en/latest/?badge=latest\n :alt:\n\n.. |coverage-shield| image:: https://codecov.io/gh/rhpvorderman/sequali/graph/badge.svg?token=MSR1A6BEGC\n :target: https://codecov.io/gh/rhpvorderman/sequali\n :alt:\n\n.. |zenodo-shield| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10854010.svg\n :target: https://doi.org/10.5281/zenodo.10854010\n :alt:\n\n|python-version-shield| |conda-version-shield| |python-install-version-shield|\n|license-shield| |docs-shield| |coverage-shield| |zenodo-shield|\n\n========\nSequali\n========\n\n.. introduction start\n\nSequence quality metrics for FASTQ and uBAM files.\n\nFeatures:\n\n+ `MultiQC <https://multiqc.info>`_ support since MultiQC version 1.22.\n+ Low memory footprint, small install size and fast execution times.\n+ Informative graphs that allow for judging the quality of a sequence at\n a quick glance.\n+ Overrepresentation analysis using 21 bp sequence fragments. Overrepresented\n sequences are checked against the NCBI univec database.\n+ Estimate duplication rate using a `fingerprint subsampling technique which is\n also used in filesystem duplication estimation\n <https://www.usenix.org/system/files/conference/atc13/atc13-xie.pdf>`_.\n+ Checks for 6 illumina adapter sequences and 17 nanopore adapter sequences\n for single read data.\n+ Determines adapters by overlap analysis for paired read data.\n+ Insert size metrics for paired read data.\n+ Per tile quality plots for illumina reads.\n+ Channel and other plots for nanopore reads.\n+ FASTQ and unaligned BAM are supported. See \"Supported formats\".\n\nExample reports:\n\n+ `GM24385_1.fastq.gz <https://sequali.readthedocs.io/en/latest/GM24385_1.fastq.gz.html>`_;\n HG002 (Genome In A Bottle) on ultra-long Nanopore Sequencing. `Sequence file download <https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/GM24385_1.fastq.gz>`_.\n+ `GM24385_1_cut.fastq.gz <https://sequali.readthedocs.io/en/latest/GM24385_1_cut.fastq.gz.html>`_;\n ``GM24385_1.fastq.gz`` processed with cutadapt:\n ``cutadapt -o GM24385_1_cut.fastq.gz --cut -64 --cut 64 --minimum-length 500 -Z --max-aer 0.1 GM24385_1.fastq.gz``.\n The resulting file has 64 bp cut off from both its ends and after that\n filtered for a minimum length of 500 and a maximum average error rate of 0.1.\n+ `21C125_R1.fastq.gz <https://sequali.readthedocs.io/en/latest/21C125_R1.fastq.gz.html>`_;\n Illumina NovaSeq X paired-end sequencing of *Campylobacter jejuni*. ENA accession:\n `ERR11204024 <https://www.ebi.ac.uk/ena/browser/view/ERR11204024>`_.\n\n.. introduction end\n\nFor more information check `the documentation <https://sequali.readthedocs.io>`_.\n\nSupported formats\n=================\n\n.. formats start\n\n- FASTQ. Only the Sanger variation with a phred offset of 33 and the error rate\n calculation of 10 ^ (-phred/10) is supported. All sequencers use this\n format today.\n\n - Paired end sequencing data is supported.\n - For sequences called by illumina base callers an additional plot with the\n per tile quality will be provided.\n - For sequences called by guppy additional plots for nanopore specific\n data will be provided.\n- unaligned BAM. Any alignment flags are currently ignored.\n\n - For uBAM data as delivered by dorado additional nanopore plots will be\n provided.\n\n.. formats end\n\nInstallation\n============\n\n.. installation start\n\nInstallation via pip is available with::\n\n pip install sequali\n\nSequali is also distributed via bioconda. It can be installed with::\n\n conda install -c conda-forge -c bioconda sequali\n\n.. installation end\n\nQuickstart\n==========\n\n.. quickstart start\n\n.. code-block::\n\n sequali path/to/my.fastq.gz\n\nThis will create a report ``my.fastq.gz.html`` and a json ``my.fastq.gz.json``\nin the current working directory.\n\n.. quickstart end\n\nFor all command line options checkout the\n`usage documentation <https://sequali.readthedocs.io/#usage>`_.\n\nFor more extensive information about the module options check the\n`documentation on the module options\n<https://sequali.readthedocs.io/#module-option-explanations>`_.\n\nAcknowledgements\n================\n\n.. acknowledgements start\n\n+ `FastQC <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_ for\n its excellent selection of relevant metrics. For this reason these metrics\n are also gathered by Sequali.\n+ The matplotlib team for their excellent work on colormaps. 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