Complement Module 
=================

Complement
----------

The **Complement module** complements the original genome with the assembled and polished reads, producing the completed genome file (``new_genome.fasta``).It also outputs the telomere position file (``telomere_positions.txt``), the telomere type file (``telomere_repeats_info.txt``), and density distribution plots of telomeres at the ends of each chromosome (stored in the ``telomere_plots18`` folder).

.. code:: bash

    #  -h, --help          show this help message and exit
    #  -G , --genome       Input genome file (FASTA format)
    #  --dir_contigs       Input polished contigs
    #  --dir_trim_L        Input the trimmed reads. If the conditions are not met, extract the
    #                      shortest reads.
    #  --dir_trim_R        Input the trimmed reads. If the conditions are not met, extract the
    #                      shortest reads.
    #  -L , --lgsreads     Long-read sequencing data
    #  -W , --wgs1         Path to WGS reads (read 1)
    #  -w , --wgs2         Path to WGS reads (read 2)
    #  -N , --NextPolish   Path to NextPolish tool
    #  -m , --motif        Telomeric repeats sequences, e.g., plant: CCCTAAA(TTTAGGG), animal:
    #                      TTAGGG(CCCTAA), etc.
    #  -M , --motif_num    Input the number of bases of the telomere motif
    #  --Normal            Execute the command according to the general process
    #  --dir_Max           Select the telomere reads obtained by polishing the longest reads to
    #                      add to the genome
    #  --dir_Min           Select the telomere reads obtained by polishing the shortest reads
    #                      to add to the genome
    #  -t , --threads      Number of threads to use (default: 20)


    $ telocomp_Complement  --Normal \
                           -G geonome.fasta \
                           --dir_contigs files_NP \
                           --dir_trim_L trim_L \
                           --dir_trim_R trim_R \
                           -L HiFi.fastq.gz \
                           -W WGS_f1.fq.gz \
                           -w WGS_r2.fq.gz -t 50 \
                           -N /PATH/NextPolish \
                           -m CCCTAAA -M 7 

Example
-------

The following pictures show the left and right ends of chromosome 2 of `Morus notabilis`.Telomere density distribution diagram of chromosome ends with telomere complementation（The following pictures show the left and right ends of chromosome 2).

Telomere density plot at the left end :

.. figure:: ../images/test_L_telomere.png
    :scale: 48 %
    :align: center


Telomere density plot at the right end:

.. figure:: ../images/test_R_telomere.png
    :scale: 48 %
    :align: center