Quality Assessment of Bins in Gut Microbiome Metagenomic Processing Pipeline
Presenter Type
UNO Undergraduate Student
Major/Field of Study
Bioinformatics
Advisor Information
Jonathan B. Clayton
Location
CEC RM #201/205/209
Presentation Type
Poster
Poster Size
48x36 inches
Start Date
22-3-2024 2:30 PM
End Date
22-3-2024 3:45 PM
Abstract
The study of the gut microbiome and its impact on overall health is of great interest in the scientific community. Gut microbiome studies assess the microorganisms that live in the gut of the organism of focus (i.e., host), which in this study is the common marmoset (Callithrix jacchus). This is accomplished by taking a sample from the gut (i.e., fecal sample) and performing shotgun sequencing, which yields the genomic information of the bacteria and other microbes in the sample as well as genomic data of the host. The host genome (marmoset) is typically removed as the focus of the study is the microbiome. BugSeq-er2 is a shotgun metagenomic assembly pipeline utilized in assembling and identifying the microbes in the gut of the marmosets used in this study. One step of BugSeq-er2 is binning, which is a method of associating overlapping DNA segments, called contigs, that are likely to be from the same organism in a sample. In this research, I have used CheckM to assess the quality of the bins that BugSeq-er2 produces. A variety of parameters have been tested and analyzed with CheckM to determine the best quality data based on completeness and contamination measures. As a result of this parameter optimization, a quality assessment and control step will be added to this pipeline to ensure the data collected is high quality and uncontaminated.
Quality Assessment of Bins in Gut Microbiome Metagenomic Processing Pipeline
CEC RM #201/205/209
The study of the gut microbiome and its impact on overall health is of great interest in the scientific community. Gut microbiome studies assess the microorganisms that live in the gut of the organism of focus (i.e., host), which in this study is the common marmoset (Callithrix jacchus). This is accomplished by taking a sample from the gut (i.e., fecal sample) and performing shotgun sequencing, which yields the genomic information of the bacteria and other microbes in the sample as well as genomic data of the host. The host genome (marmoset) is typically removed as the focus of the study is the microbiome. BugSeq-er2 is a shotgun metagenomic assembly pipeline utilized in assembling and identifying the microbes in the gut of the marmosets used in this study. One step of BugSeq-er2 is binning, which is a method of associating overlapping DNA segments, called contigs, that are likely to be from the same organism in a sample. In this research, I have used CheckM to assess the quality of the bins that BugSeq-er2 produces. A variety of parameters have been tested and analyzed with CheckM to determine the best quality data based on completeness and contamination measures. As a result of this parameter optimization, a quality assessment and control step will be added to this pipeline to ensure the data collected is high quality and uncontaminated.