Comparing assemblies to the reference
=====================================

The Quast program can be used to generate similar metrics as the
assemblathon\_stat.pl script, pluss some more and some visualisations.

+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
| Program   | Options           | Explanation                                                                                                                   |
+===========+===================+===============================================================================================================================+
| Quast     |                   | Evaluating genome assemblies                                                                                                  |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | -o                | name of output folder                                                                                                         |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | -R                | Reference genome                                                                                                              |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | -G                | File with positions of genes in the reference (see manual)                                                                    |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | -T                | number of threads (cpu's) to use                                                                                              |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | sequences.fasta   | one or more files with assembled sequences                                                                                    |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | -l                | comma-separates list of names for the assemblies, e.g. "assembly 1", "assembly 2" (in the same order as the sequence files)   |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | --scaffolds       | input sequences are scaffolds, not contigs. They will be split at 10 N's or more to analyse contigs ('broken' assembly)       |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | --est-ref-size    | estimated reference genome size (when not provided)                                                                           |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+
|           | --gene-finding    | apply GenemarkS for gene finding                                                                                              |
+-----------+-------------------+-------------------------------------------------------------------------------------------------------------------------------+

See the manual for information on the output of Quast:
http://quast.bioinf.spbau.ru/manual.html#sec3

Running Quast
^^^^^^^^^^^^^

TIP: log in to the cod3 server using the ``Y`` flag with ``ssh``:

::

    ssh -Y username@cod3.hpc.uio.no

This becomes useful at the end.

Set up quast:

::

    module load quast/3.0

On the server, make a folder called ``quast`` and move into it. Then
run:

::

    quast.py -T 2 \
    -o out_folder_name \
    -R /data/assembly/NC_000913_K12_MG1655.fasta \
    -G /data/assembly/e.coli_genes.gff \
    ../path/to/assembly1.fasta \
    ../path/to/assembly2.fasta \
    -l "Assembly 1, Assembly 2"

Note that the ``--scaffold`` option is not used here for simplification.
Also, make sure you name the assemblies (``-l``) in the same order as
you give them to quast!

Quast output
^^^^^^^^^^^^

Quast will produce a html report file ``report.html``. If you have
logged in to the cod3 server using ``ssh -Y`` you can now type

::

    cd out_folder_name
    firefox report.html

Otherwise, download the report *and* the ``report_html_aux`` folder to
your PC and open the ``html`` file in your browser.

Hover over the row names to get a description. Also have a look at the
'Extended report'.

Alternatively, have a look at the report.pdf file (it has a few more
plots).