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).

#  -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 :

Telomere density plot at the right end: