GapClosure program to patch gaps in genome assemblies

Program GapClosur 03.12.2024Author: O. Reva (oleg.reva@up.ac.za)Last time modified: March 12, 2024Assisted with OpenAI ChatGPT4 python run.py - show command prompt menupython run.py [-arguments]python run.py -h / -H / --help - show this helppython run.py -v / -V / --version - show version Arguments:       -t:       # generic subword within subgect sequence and gaps file.       -r:       # name of the referense file.       -s:       # name of the subject sequence file or a unique marker subword;                 # If a marker is specified, the subject sequence file name muct contain                  # both: the marker and the generic subwords.       -g:       # name of the gaps file or a unique marker subword;                 # If a marker is specified, the subject sequence file name muct contain                  # both: the marker and the generic subwords.                 # This file is an output file of Mauve->Tools->Export->Export Gaps.       -m:       # Minimal length of gaps, 10 by default.       -p:       # Shows a plot created by matplotlib.                 # Library matplotlib must be installed.       -o:       # /optional/ Name of the output sequence file.                  # If not specified, generic name will be used.       -x:       # 'input' by default. All input files must be placed here.       -y:       # 'output' by default. Output files are stored here.  Currently, folder 'input' contains 3 example files:ID003.reference.fa - reference sequence file;IB011.subject.fa - subject sequence file;IB011.gaps.txt - text file containing a list of gaps in sequence IB011compared to sequence ID003. Program Mauve (darlinglab.org) was used to align whole genome sequences of S. aureus isolates against each other using the function File -> Align with progressiveMauve. The reference sequence must be placed first in the list, followed by the subject sequence. After the sequence alignment is complete, use the command Tools -> Export -> Export Gaps to save the gaps to a file that this program utilizes.  The program uses the gaps file to identify locations of insertions in the reference sequence that are absent in the subject sequence and fills these gaps in the subject sequence by patching them from the reference sequence. In the next step, the patches must be verified by mapping the initial DNA reads against the resulting sequence stored in the 'output' folder. This program was used for the first time in the paper titled  "Staphylococcus aureus associated with post-operative wound infections in Western Kenya reveals genomic hotspots for pathogen evolution" by Mogoi et al., 2024.