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.. _software-details:
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.. TODO: complete this page
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Software Information
********************
      
This is a general guide for the software that we employed along the ``XICRA`` pipeline.

.. contents::

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.. _fastqc-description:
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FastQC
======

FastQC :cite:`fastqc` is a quality control tool for high throughput sequence data. It aims to provide a simple 
way to do some quality control checks on raw sequence data coming from high throughput sequencing 
pipelines. It provides a modular set of analysis which you can use to give a quick impression of 
whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

- Import of data from BAM, SAM or FastQ files (any variant)

- Providing a quick overview to tell you in which areas there may be problems

- Summary graphs and tables to quickly assess your data

- Export of results to an HTML based permanent report

- Offline operation to allow automated generation of reports without running the interactive application

Read further information about FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/


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.. _cutadapt-description:
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Cutadapt
========


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.. _STAR-description:
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STAR
====


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.. _featureCounts-description:
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Feature counts
==============



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.. _mirTop-description:
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mirTop
======


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.. _miraligner-description:
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Miraligner
==========

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.. _mintmap-description:
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MINTmap
=======


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.. _sRNAbench-description:
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sRNAbench
=========


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.. _optimir-description:
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Optimir
=======