Course Info

Applied Genome Analysis
Fall Semester 2022 (10/2022)
Term Project
UGA GACRC - Sapelo2

Contact info

Summer Blanco ([email protected])
PhD Student, Department of Plant Biology
Leebens-Mack & Chang Labs
University of Georgia

About

This repository contains the scripts & results for analyzing Illumina shotgun sequencing data for Geranium maculatum. Leaf tissue was collected by Dr.Shu-Mei Chang (SMC). DNA was extracted using a Qiagen kit by Summer Blanco (SB) & SMC. Library preparation & sequencing was done by Novogene. Bioinformatics analyses were conducted by SB with guidance from Dr. Jim Leebens-Mack, Dr. Casey Bergman, and Jingxuan Chen.

Pipeline:

1. FastQC & MultiQC pre-trim
2. Trimmomatic
3. FastQC & MultiQC post-trim
4. Jellyfish & GenomeScope
5. GetOrganelle & NOVOPlasty
6. SAMtools/BCFtools & IGV
7. Meraculous
8. QUAST

File structure

k-mer analysis

genomescope

Contains 7 folders: k19, k21, k23, k25, k27, k29, k31
Each folder contains:
-model.txt
-plot.log.png (GenomeScope visualization)
-plot.png (GenomeScope visualization)
-progress.txt
-summary.txt

jellyfish_histograms

Contains 7 files:
-19test.histo
-k21test.histo
-k23test.histo
-k25test.histo
-k27test.histo
-k29test.histo
-k31test.histo

Each file used with GenomeScope to generate kmer visualization.

plastome

Bandage

-BANDAGEgraph.png (Bandage visualization from GetOrganelle)
-extended_K115.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg (Assembly graph from GetOrganelle)

Contigs

-Contigs_1_NovoTest.fasta (Contigs from NOVOPlasty)
-embplant_pt.K115.scaffolds.graph1.1.path_sequence.fasta (Scaffolds from GetOrganelle)

Mapping

-G_incanum_plastomesequence.fa
-G_incanum_plastomesequence.fasta
-G_incanum_plastomesequence.fasta.fai -GIncanumVsGmaculatum.xml

Mummer Plots

-GOnucmer.png
-novonucmer.png

QC

pretrimQC

Contains 5 files:
-OT1_CKDN220054653-1A_HF33VDSX5_L1_1_fastqc.html
-OT1_CKDN220054653-1A_HF33VDSX5_L1_2_fastqc.html
-multiqc_report.html
-OT1_CKDN220054653-1A_HF33VDSX5_L1_1_fastqc.zip
-OT1_CKDN220054653-1A_HF33VDSX5_L1_2_fastqc.zip

MultiQC report contains summary for 2 raw read files.

trimmedQC

Contains 5 files:
-OT1_CKDN220054653-1A_HF33VDSX5_L1_R1_paired_fastqc.html
-OT1_CKDN220054653-1A_HF33VDSX5_L1_R2_unpaired_fastqc.html
-OT1_CKDN220054653-1A_HF33VDSX5_L1_R1_unpaired_fastqc.html
-multiqc_report.html
-OT1_CKDN220054653-1A_HF33VDSX5_L1_R2_paired_fastqc.html

MultiQC report contains summary for 2 trimmed read files.

scripts

Contains 3 files:

-G_maculatum.sh
-G_maculatum.config
-config.txt