.. _framework-tools-genomics:

==================
Genomics tools
==================

Quality control
===============

+----------------------------------------------------------------------------------+---------+----------------------------------------------------------------------------+
| Name                                                                             | Version | Galaxy wrapper                                                             |
+==================================================================================+=========+============================================================================+
| `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_            | 0.67    | `fastqc <https://toolshed.g2.bx.psu.edu/view/devteam/fastqc/>`_            |
+----------------------------------------------------------------------------------+---------+----------------------------------------------------------------------------+
| PRINSEQ :cite:`schmieder_quality_2011`                                           | 0.20.4  | `prinseq <https://toolshed.g2.bx.psu.edu/view/iuc/prinseq>`_               |
+----------------------------------------------------------------------------------+---------+----------------------------------------------------------------------------+
| `Trim Galore! <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>`_ | 0.4.3   | `trim_galore <https://toolshed.g2.bx.psu.edu/view/bgruening/trim_galore>`_ |
+----------------------------------------------------------------------------------+---------+----------------------------------------------------------------------------+
| Trimmomatic :cite:`bolger2014trimmomatic`                                        | 0.36    | `trimmomatic <https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic>`_  |
+----------------------------------------------------------------------------------+---------+----------------------------------------------------------------------------+
| MultiQC :cite:`ewels2016multiqc`                                                 | 0.20.4  | `multiqc <https://toolshed.g2.bx.psu.edu/view/iuc/multiqc>`_         |
+----------------------------------------------------------------------------------+---------+----------------------------------------------------------------------------+

Clustering
==========
+------------------------------------------------+---------+--------------------------------------------------------------------------------------------+
| Name                                           | Version | Galaxy wrapper                                                                             |
+================================================+=========+============================================================================================+
| CD-HIT :cite:`fu_cd-hit:_2012,li_cd-hit:_2006` | 4.6.4   | `cdhit <https://toolshed.g2.bx.psu.edu/view/bebatut/cdhit/>`_                              |
+------------------------------------------------+---------+--------------------------------------------------------------------------------------------+
| Format CD-HIT output                           |         | `format_cd_hit_output <https://toolshed.g2.bx.psu.edu/view/bebatut/format_cd_hit_output>`_ |
+------------------------------------------------+---------+--------------------------------------------------------------------------------------------+

Sorting and Prediction
======================
+--------------------------------------------+---------+------------------------------------------------------------------------+
| Name                                       | Version | Galaxy wrapper                                                         |
+============================================+=========+========================================================================+
| SortMeRNA :cite:`kopylova_sortmerna:_2012` | 2.1b    | `sortmerna <https://toolshed.g2.bx.psu.edu/view/rnateam/sortmerna>`_   |
+--------------------------------------------+---------+------------------------------------------------------------------------+
| FragGeneScan :cite:`rho2010fraggenescan`   | 1.30    | `fraggenescan <https://toolshed.g2.bx.psu.edu/view/iuc/fraggenescan>`_ |
+--------------------------------------------+---------+------------------------------------------------------------------------+

Similarity search and alignment
===============================

+--------------------------------------------------------+---------+----------------------------------------------------------------------------------+
| Name                                                   | Version | Galaxy wrapper                                                                   |
+========================================================+=========+==================================================================================+
| NCBI BLAST :cite:`camacho_blast+:_2009,cock_ncbi_2015` | 2.2.30  | `ncbi_blast_plus <https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus>`_ |
+--------------------------------------------------------+---------+----------------------------------------------------------------------------------+
| Diamond :cite:`buchfink_fast_2015`                     | 0.8.24  | `diamond <https://toolshed.g2.bx.psu.edu/view/bgruening/diamond>`_               |
+--------------------------------------------------------+---------+----------------------------------------------------------------------------------+
| HMMER3 :cite:`finn2011hmmer`                           | 3.1b2   | `hmmer3 <https://toolshed.g2.bx.psu.edu/view/iuc/hmmer3>`_                       |
+--------------------------------------------------------+---------+----------------------------------------------------------------------------------+


Mapping
=======
+--------------------------------------------------------+---------+------------------------------------------------------------------+
| Name                                                   | Version | Galaxy wrapper                                                   |
+========================================================+=========+==================================================================+
| BWA :cite:`li_fast_2009,li_fast_2010,li_aligning_2013` | 0.7.12  | `bwa <https://toolshed.g2.bx.psu.edu/view/devteam/bwa>`_         |
+--------------------------------------------------------+---------+------------------------------------------------------------------+
| Bowtie2 :cite:`langmead2012fast`                       | 2.3.2   | `bowtie2 <https://toolshed.g2.bx.psu.edu/view/devteam/bowtie2>`_ |
+--------------------------------------------------------+---------+------------------------------------------------------------------+




.. rubric:: References

.. bibliography:: /assets/references.bib
   :cited:
   :style: plain
   :filter: docname in docnames