This repository contains data, scripts, and analysis results for the research project titled "Complete Genome Sequence of Acetobacteraceae Strain." The project involves the genome sequencing and analysis of a novel Bombella strain isolated from the gut microbiota of Geniotrigona thoracic stingless bees in Tenom, Malaysia.
The MGEs directory contains scripts for identifying and summarizing Mobile Genetic Elements (MGEs).
01.00.identify_MGEs.sh: Script for identifying MGEs.02.00.summarizing_MGEs.sh: Script for summarizing MGEs.assembly_names.out: names of input assemblies to run script 01.00 for more than one genome in parallel using arrays.logpipeline: Directory containing logs for the pipeline.
This directory contains scripts and analysis for assembling, polishing and annotating Bacterial genome
strain_12_filtered_readLength.png: PNG file showing read length stats for filtered reads.strain_12_raw_readLength.png: PNG file showing read length stats for raw reads.
graph.png: PNG file displaying the assembly graph.
00.01_CopyFiles.sh: Script for copying files.00.02_readLength_rawReads.sh: Script for analyzing raw read lengths.01.00_filtlong.sh: Script for filtering long reads.02.00_Genome_Assembly.Flye.sh: Script for genome assembly using Flye.03.00_Genome_Assembly.ONT_Polishing.v2.sh: Script for ONT polishing.03.01_Genome_Assembly.illumina_Polishing.sh: Script for Illumina polishing.03.02_Genome_Assembly.Polished.QC.sh: Script for quality control on polished assembly.03.03_QuickCheck.sh: Script for quick checks on assembly.04.00_Genome_Assembly.CheckM.sh: Script for assembly quality check using CheckM.05.00_Genome_Assembly.Annotation_DRAM.sh: Script for genome annotation using DRAM.06.00_Genome_Assembly.GTBD-Tk.sh: Script for taxonomy assignment using GTDB-Tk.logpipeline: Directory containing logs for the entire pipeline.plot_read_length.R: R script for plotting read length stats (see dir: 01_Analysis)Readme: Directory containing additional readme files.