I will perform chloroplast genome assembly and comparative analysis

About This Gig

Are you looking for a professional bioinformatician to handle your plant genomics data? I specialize in Chloroplast Genome (Plastome) assembly and comprehensive Comparative Genomic Analysis. I provide publication-ready results with high-resolution figures tailored for SCI journals.

What I offer in this Gig:

1. Genome Assembly & Annotation

• De novo Assembly: High-quality circular genome assembly from Illumina, PacBio, or Nanopore raw reads using GetOrganelle or NOVOPlasty.
• Precise Annotation: Gene prediction (CDS, rRNA, tRNA) using GeSeq/PGA with manual curation to ensure accuracy.

2. Comparative Genomic Analysis

• IR Boundary Analysis: Contraction and expansion of Inverted Repeats (Junction sites).
• Repeat Identification: SSRs (Simple Sequence Repeats) and Long Repeats analysis.
• Nucleotide Diversity: Sliding window analysis to identify highly divergent regions (Pi).
• Selection Pressure: Calculating Ka/Ks ratios for protein-coding genes.

3. Phylogeny & Visualization

• Phylogenetic Trees: Constructing Maximum Likelihood (ML) or Bayesian (BI) trees using IQ-TREE or MrBayes.
• Pro Figures: High-resolution circular maps (OGDRAW), synteny plots, and comparative alignment visuals.