Genome-Analysis

Genome Analysis Project

Project Plan

Aim: "Dead Zones" or areas of ocean with seasonal to long-term low dissolved oxygen (DO) concentrations are becoming increasingly more frequent. This study focuses on one of the largest costal dead zones on the northern Gulf of Mexico. The low DO levels are due to eutrophication-enhanced bacterioplankton respiration as well as strong seasonal stratification. I am going to assemble genomes of becterioplankton collected from the northern Gulf of Mexico dead zone by Thrash et al. as described in Metabolic roles of uncultivated bacterioplankton lineages in the Northern Gulf of Mexico “dead zone”. Analysis will include metagenome assembly, binning to create individual genomes, as well as expression analysis and phylogenetic assignment. Knowing which species or genuses of bacerioplankton are able to live in the nGOM, in both oxic and hypoxic environment is imperative to understanding the environment. Learning more about these species, both previously described and not will help us to better understand the active biogeochemical cycling they mediate. Expression analysis conducted along with functional annotation gives even more insight as we can see the metabolic pathways present and how they contribute to the environment.

Workflow

Analysis	Program	Output	Expected Run Time	Expected Deadline	Completed
Reads Quality Control	FastQC	.html	~15 min	April 7th	Yes
RNA Trimming	Trimmomatic	fastq	~30 min	April 7th	Yes
DNA Assembly	Megahit	./megahit_out with output directory .contigs.fa with contigs	~6 h	April 7th	Yes
Assembly Evaluation	QUAST	.txt .pdf	~ 45 min	April 14th	Yes
DNA Alignment	BWA	.bam	~ 4-6 h	April 21st	Yes
Binning	Metabat	.fasta for each bin	<30 min	April 21st	Yes
Binning Evaluation	CheckM	output report	~2 h	April 21st	Yes
RNA Alignment	BWA	.sam	~ 4-6 h	April 21st	Yes
Annotation	Prokka	GFF file with annotations GenBank file with sequences	~ 1 h	April 28th	Yes
Phylogenetic Placement	PhyloPhlan	top SGBs closest SGB, GGB, FGB reference genomes, and "all vs. all" matrix of all pairwise Mash distances	~6 h	April 28th	Yes
Expression Analysis	HTseq	.txt with read count table	~6 h	April 28th	Yes
Extra Analysis: Abundance of Organisms	BWA	.bam	~ 4-6 h	May 12th	Yes

Data Management System

├── genome_analyses
    ├── 01_reads_quality_control  
    │       └── fastqc_trimmed_RNA_script 
    │       └── slurm-7528571.out 
    │   ├── fastqc_DNA_results
    │   ├── fastqc_RNA_post_trim_results
    │   ├── fastqc_RNA_pre_trim_results
    ├── 02_RNA_trimming
    │       └── adapter_sequences
    │       └── slurm-7528563.out
    │       └── trimmomatic_script
    │   ├── trimmed_RNA
    ├── 03_DNA_assembly
    │       └── megahit_script
    │       └── slurm-7723214.out
    │   ├── DNA_assembly_results
    ├── 04_assembly_evaluation 
    │       └── quast_script
    │       └── slurm-7731177.out
    │   ├── quast_results 
    ├── 05_alignment
    │       └── bwa_results_SRR4342129.bam
    │       └── bwa_results_SRR4342133.bam
    │       └── bwa_script
    │       └── slurm-7795240.out
    ├── 06_binning
    │       └── change_bin_names_script
    │       └── depth.txt
    │       └── metabat_script
    │       └── slurm-7797909.out
    │       └── slurm-7799427.out
    │   ├── bins
    ├── 07_binning_evaluation
    │       └── checkm_qa
    │       └── checkm_qa_script
    │       └── checkm_script
    │       └── slurm-7799916.out
    │       └── slurm-7827270.out
    │   ├── CheckM_data
    │   ├── checkm_results
    ├── 08_RNA_mapping
    │       └── bwa_script_for_loop 
    │       └── bwa_script_for_loop_sample_2
    │       └── slurm-7855951.out
    │       └── slurm-7855966.out
    ├── 09_annotation
    │       └── prokka_script
    │       └── rename_annotation
    │       └── slurm-7852786.out
    │   ├── 1_prokka_results 
    │   ├── ...  
    │   ├── 49_prokka_results  
    │   ├── renamed_annotations  
    ├── 10_phylo_placement
    │       └── make_annotation_folder 
    │       └── phylophlan_conda_script
    │       └── slurm-7856958.out
    │   ├── phylogeny_results  
    ├── 11_expression_analysis
    │       └── 1_SRR4342137_expression_results.txt
    │       └── ...
    │       └── 49_SRR4342139_expression_results.txt
    │       └── htseq_script
    │       └── slurm-7856869.out
    ├── 12_abundance_of_bins
    │       └── bwa_script
    │   ├── mapping to bins 
    ├── DNA_trimmed
    ├── RNA_untrimmed