.. _preprocess:

==========================================
``preprocess``
==========================================

.. contents::

Overview
-------------
``preprocess`` is a program within the sortseq_tools package which takes raw,
paired end FASTA or FASTQ files as inputs and subjects them to quality score 
filtering, barcode filtering, and filtering for paired end reads which align in
the overlap region through the fastx toolkit. After filtering with this module
you must use the gatherseqs function to put the files into a format that sortseq_tools
can use.

After you install `sortseq_tools`_, this program will be available to run at the command line. 

Command-line usage
---------------------
.. argparse::
   :module: sortseq.sortseq_for_doc
   :func: parser
   :prog: sortseq
   :path: preprocess

   

   
Examples
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.. include:: weblinks.txt