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https://github.com/epruesse/sina

SINA - Reference based multiple sequence alignment
https://github.com/epruesse/sina

16s alignment bioinformatics rrna sequence silva

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SINA - Reference based multiple sequence alignment

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README 

        
SINA - reference based multiple sequence alignment

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|latest| |Bioconda| |downloads| |TravisCI| |CircleCI| |Read the Docs| |Codecov|



.. |latest| image:: https://img.shields.io/github/release/epruesse/SINA/all.svg?label=latest

.. |release| image:: https://img.shields.io/github/release/epruesse/SINA.svg

.. |Bioconda| image:: https://img.shields.io/conda/vn/Bioconda/sina.svg

   :target: https://bioconda.github.io/recipes/sina/README.html

.. |TravisCI| image:: https://img.shields.io/travis/epruesse/SINA.svg?label=build%20(TravisCI)

   :target: https://travis-ci.org/epruesse/SINA

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   :target: https://circleci.com/gh/epruesse/SINA

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.. |Read the Docs| image:: https://img.shields.io/readthedocs/sina/latest.svg

   :target: https://readthedocs.org/projects/sina/builds

.. |downloads| image:: https://img.shields.io/conda/dn/bioconda/sina.svg?style=flat



SINA aligns nucleotide sequences to match a pre-existing MSA using

a graph based alignment algorithm similar to PoA. The graph approach

allows SINA to incorporate information from many reference sequences

building without blurring highly variable regions. While

pure NAST implementations depend highly on finding a good match in

the reference database, SINA is able to align sequences relatively

distant to references with good quality and will yield a robust result

for query sequences with many close reference.



Features

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- Speed. Aligning 100,000 full length rRNA against the SILVA NR takes 40 minutes on a mid-sized 2018 desktop computer. Aligning 1,000,000 V4 amplicons takes about 60 minutes.

- Accuracy. SINA is used to build the SILVA_ SSU and LSU rRNA databases.

- Classification. SINA includes an LCA based classification module.

- ARB. SINA is able to directly read and write ARB_ format files such as distributed by the SILVA_ project.



.. _SILVA: https://www.arb-silva.de

.. _ARB: https://www.arb-home.de



Online Version

--------------



An online version for submitting small batches of sequences is made

available by the SILVA_ project as part of their

`ACT: Alignment, Classification and Tree Service `_.

In addition to SINA's alignment and classification stages, ACT allows directly building

phylogenetic trees with RAxML or FastTree from your sequences and (optionally)

additional sequences chosen using SINA's add-neighbors feature.



Installing SINA

---------------



The preferred way to install SINA locally is via `Bioconda `_.

If you have a working Bioconda installation, just run::



    conda create -n sina sina

    conda activate sina



Alternatively, self-contained images are available at

https://github.com/epruesse/SINA/releases. Choose the most recent ``tar.gz``

appropriate for your operating system and unpack::



   tar xf sina-1.7.3-dev-dev-linux.tar.gz

   cd sina-1.7.3-dev-dev

   ./sina



Documentation

-------------



The full documentation is available at https://sina.readthedocs.io.



The algorithm is explained in the paper:



  Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner; *SINA: Accurate

  high-throughput multiple sequence alignment of ribosomal RNA

  genes.* Bioinformatics 2012; 28 (14): 1823-1829.

  `doi:10.1093/bioinformatics/bts252 `_