Assembly improvement using REAPR
================================

From the REAPR website: > REAPR is a tool that evaluates the accuracy of
a genome assembly using mapped paired end [and mate pair] reads, without
the use of a reference genome for comparison. It can be used in any
stage of an assembly pipeline to automatically break incorrect scaffolds
and flag other errors in an assembly for manual inspection. It reports
mis-assemblies and other warnings, and produces a new broken assembly
based on the error calls.

REAPR can take both paired end reads mapped to the assembly, and mate
pairs, Here we will restrict the analysis to the mate pairs

Set up the environment
^^^^^^^^^^^^^^^^^^^^^^

Load the following modules:

::

    module load reapr

Using REAPR
~~~~~~~~~~~

-  ``cd`` to folder with assembly fasta file
-  Run REAPR as follows:

::

    reapr pipeline ASSEMBLY.FASTA bwa/map_mp.sorted.bam reapr_out >reapr.out 2>&1

-  REAPR wil start producing some files in the ``reapr_out`` folder, and
   then take a long time in the ``[REAPR pipeline] Running stats``
   stage, while adding data to the file ``01.stats.per_base.gz``.
-  After that, it is finished quite quickly.

REAPR output
^^^^^^^^^^^^

-  The ``reapr_out`` folder and the folder ``reapr_out/00.Sample`` has a
   few PDFs that may be of interest
-  The file ``05.summary.report.txt`` has a lot of information an what
   REAPR did with the assembly. Error-free bases have at least 5X
   perfect and unique coverage of paired end reads. For more
   information, check the REAPR manual.
-  The file ``04.break.broken_assembly_bin.fa`` is a revised version of
   *only those* scaffolds from the assembly that were broken at places
   REAPR determined an error
-  The file ``04.break.broken_assembly.fa`` is a revised version of the
   assembly, with all scaffolds, whether they were broken or not. Broken
   contigs have their name changed: ``REAPR_bin`` is added to the
   beginning, and the *last two numbers in the name* are the coordinates
   where reapr broke the assembly
-  Finally, There is a ``gff`` file with the detected errors called
   ``03.score.errors.gff.gz``. You can add this file to the browser, but
   it needs a small modification: all spaces in the file need to be
   replaced by underscores (otherwise only the first 'word' of each line
   will be shown in the browser). For this, we use the tool ``zcat`` to
   extract the information of the compressed file, and pipe the text
   into the ``sed`` program to replace all spaces with the ``_`` sign:

::

    zcat 03.score.errors.gff.gz |sed 's/ /_/g' >03.score.errors_nospaces.gff

In this file, regions where reapr broke the assembly are marked with
``FCD_failure``. You can now add the ``03.score.errors_nospaces.gff``
file to IGV (after downloading it). Find the regions where reapr broke
the assembly (using the ``04.break.broken_assembly.fa`` file) and see
whether you agree with reapr's conclusion.