Assembly Module

The Assembly module primarily assembles the reads processed by the Filter module, and outputs the final assembly results to the Files_NP directory.

# optional arguments:
# -h, --help          show this help message and exit
# --dir_IN_L          Directory containing left-aligned reads (FASTA format)
# --dir_IN_R          Directory containing right-aligned reads (FASTA format)
# --flye              Flye assembly module (default: True)
# --assemble, -a      Assemble using an alternative assembly module
# -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
# -t , --threads      Number of threads to use (default: 20)

# The Assemble module can be adjusted using the following parameters
# --min_overlap       Minimum overlap length (default: 50)
# --error_rate        Error rate for assembly (default: 0.15)
# --kmer_size         K-mer size (default: 15)


# Flye assembly module (default assembly)
$ telocomp_Assembly --dir_IN_L trim_L \
                    --dir_IN_R trim_R \
                    -L HiFi.fq.gz \
                    -W WGS_f1.fq.gz \
                    -w WGS_r2.fq.gz \
                    -N /PATH/NextPolish -t 50

# assemble assembly module
$ telocomp_Assembly --dir_IN_L trim_L \
                    --dir_IN_R trim_R \
                    -L HiFi.fq.gz \
                    -W WGS_f1.fq.gz \
                    -w WGS_r2.fq.gz \
                    -N /PATH/NextPolish \
                    -t 50 --assemble

Note: If reads at a chromosome end cannot be assembled, TeloComp defaults to selecting the shortest reads to supplement the reference genome.