About
Plant Genome Insights provides high-level, custom bioinformatics analyses for plant genomics and transcriptomics projects. We focus on transforming raw sequencing data into robust, biologically meaningful results suitable for scientific publication and advanced R&D applications.
We do not provide sequencing services. We work exclusively on your existing data (FASTQ, BAM, count matrices, assemblies, variant files, etc.), offering in-depth analysis, interpretation, and methodological refinement well beyond standard, sterile pipeline outputs.
What We Do
Plant Transcriptomics
• Experimental design & QC (FastQC, Trimmomatic)
• Read mapping and quantification (HISAT2, TopHat2, Bowtie2)
• Differential expression analysis (EdgeR)
• Transcriptome assembly (CLC Genomics Workbench, Trinity)
• Co-expression network analysis (WGCNA)
• Pathway/process-level interpretation (MapMan, KEGG)
• Gene function and annotation (Blast2GO, BLAST)
• Integration with phenotypic, physiological, or metabolic traits
Plant Genomics
• Genome annotation & refinement (Augustus, SNAP, GeneID, GlimmerHMM, EvidenceModeler, PASA, BUSCO)
• Repeat annotation, Transposable Elements analysis (EDTA, RepeatExplorer2, DANTE)
• Comparative genomics & synteny (MCScanX)
• Variant calling (GATK, VarScan2, VCFTools)
• Phylogenetics (MEGA)
• Gene sequence alignment (Clustal, BWA)
• Data format manipulation (SAMtools, BEDTools, EMBOSS)