panISa
======
panISa is a software identifying insertion sequence (IS) on resequencing
data (bam file) in bacterial genomes.
Idea
----
The panISa software searches for Insertion Sequences on NGS data ab
initio (i.e. with a database-free approach) in bacterial genomes
from short read data. Briefly, the software identifies a signature
of insertion in the alignment by counting clipped reads on the start
and end positions of the potential IS. These clipped reads overlap
the direct repeats due to IS insertion. Finally, using a
reconstruction of the beginning of both sides of the IS (IRL and IRR), panISa
validates the IS by searching for inverted repeat regions.
.. image:: principe.png
:alt: Principe of panISa
:align: center
Requirements and Installation
-----------------------------
Conda installation
~~~~~~~~~~~~~~~~~~
You can easy install panisa program and requirements using conda:
.. code-block:: bash
conda install -c bioconda panisa
Requirements
~~~~~~~~~~~~
The program used the python library **pysam** (>=0.9) and **request** (>=2.12)
You need to install `the emboss package <http://emboss.sourceforge.net>`_
In debian, type:
.. code-block:: bash
sudo apt-get install python-pysam python-requests emboss
Installation
~~~~~~~~~~~~
Download the current tarball and unzip it.
Verify the installation using the test file
.. code-block:: bash
python panISa.py test/test.bam
Alternatively, you can install from `PyPI repository <https://pypi.python.org/pypi>`_
.. code-block:: bash
pip install panisa
Command and Options
-------------------
.. code-block:: bash
python panISa.py [options] bam
Options
~~~~~~~
-h show this help message and exit
-o Return list of IS insertion by alignment [stdout]
-q Minimum alignment quality value to conserve a clipped read [20]
-m Minimum number of clipped reads to look at IS on a position [10]
-s Maximum size of direct repeat region [20bp]
-p Minimum percentage of same base to create consensus [0.8]
-v show program's version number and exit
Output
------
PanISa returns result in tabular format with the following columns:
Chromosome:
chromosome id
End position:
position of the last base of the direct repeat and the left bondary of
the potential IS (IRL)
End clipped reads:
number of clipped reads (end position)
Direct repeat:
nucleotidic sequence of the direct repeat
Start position:
position of the first base of the direct repeat and the right
bondary of the potential IS (IRR)
Start clipped reads:
number of clipped reads (start position)
Inverted repeats:
nucleotidic sequence of inverted repeats and their position
IS left sequence:
reconstruction of the left boundary of the potential IS (IRL)
IS right sequence:
reconstruction of the right boundary of the potential IS (IRR)
Validation
----------
PanISa results can be search for homology against ISFinder to find IS familly using the script ISFinder_search.py
.. code-block:: bash
python ISFinder_search.py [options] panISa results
Recommandation
--------------
panISa works well with the alignment from **bwa** software.
Citation
--------------
If you use the panISa software, please cite the following paper:
**panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.**
Treepong P, Guyeux C, Meunier A, Couchoud C, Hocquet D, Valot B.
Bioinformatics. 2018, 34(22):3795-3800.
doi: 10.1093/bioinformatics/bty479
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"description": "panISa\n======\n\npanISa is a software identifying insertion sequence (IS) on resequencing\ndata (bam file) in bacterial genomes.\n\nIdea\n----\n\nThe panISa software searches for Insertion Sequences on NGS data ab\ninitio (i.e. with a database-free approach) in bacterial genomes\nfrom short read data. Briefly, the software identifies a signature\nof insertion in the alignment by counting clipped reads on the start\nand end positions of the potential IS. These clipped reads overlap\nthe direct repeats due to IS insertion. Finally, using a\nreconstruction of the beginning of both sides of the IS (IRL and IRR), panISa\nvalidates the IS by searching for inverted repeat regions.\n\n.. image:: principe.png\n :alt: Principe of panISa\n :align: center\n\nRequirements and Installation\n-----------------------------\n\nConda installation\n~~~~~~~~~~~~~~~~~~\n\nYou can easy install panisa program and requirements using conda:\n\n.. code-block:: bash\n\n conda install -c bioconda panisa\n\nRequirements\n~~~~~~~~~~~~\n\nThe program used the python library **pysam** (>=0.9) and **request** (>=2.12)\n\nYou need to install `the emboss package <http://emboss.sourceforge.net>`_\n\nIn debian, type:\n\n.. code-block:: bash\n\n sudo apt-get install python-pysam python-requests emboss\n\nInstallation\n~~~~~~~~~~~~\n\nDownload the current tarball and unzip it.\n\nVerify the installation using the test file\n\n.. code-block:: bash\n\n python panISa.py test/test.bam\n\nAlternatively, you can install from `PyPI repository <https://pypi.python.org/pypi>`_\n\n.. code-block:: bash\n\n pip install panisa\n\n \nCommand and Options\n-------------------\n\n.. code-block:: bash\n\n python panISa.py [options] bam\n\nOptions\n~~~~~~~\n\n-h show this help message and exit\n-o Return list of IS insertion by alignment [stdout]\n-q Minimum alignment quality value to conserve a clipped read [20]\n-m Minimum number of clipped reads to look at IS on a position [10]\n-s Maximum size of direct repeat region [20bp]\n-p Minimum percentage of same base to create consensus [0.8]\n-v show program's version number and exit\n\nOutput\n------\n\nPanISa returns result in tabular format with the following columns: \n\nChromosome:\n chromosome id \nEnd position:\n position of the last base of the direct repeat and the left bondary of\n the potential IS (IRL)\nEnd clipped reads:\n number of clipped reads (end position)\nDirect repeat:\n nucleotidic sequence of the direct repeat\nStart position:\n position of the first base of the direct repeat and the right\n bondary of the potential IS (IRR)\nStart clipped reads:\n number of clipped reads (start position)\nInverted repeats:\n nucleotidic sequence of inverted repeats and their position\nIS left sequence:\n reconstruction of the left boundary of the potential IS (IRL)\nIS right sequence:\n reconstruction of the right boundary of the potential IS (IRR)\n\nValidation\n----------\n \nPanISa results can be search for homology against ISFinder to find IS familly using the script ISFinder_search.py\n\n.. code-block:: bash\n\n python ISFinder_search.py [options] panISa results\n\nRecommandation\n--------------\n\npanISa works well with the alignment from **bwa** software.\n\nCitation\n--------------\n\nIf you use the panISa software, please cite the following paper:\n\n**panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.** \nTreepong P, Guyeux C, Meunier A, Couchoud C, Hocquet D, Valot B. \nBioinformatics. 2018, 34(22):3795-3800. \n\ndoi: 10.1093/bioinformatics/bty479\n",
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