About This Blog
Welcome to Daily Bioinformatics from Jojy’s Desk — my living notebook of daily bioinformatics work, microbial ecology, MAGs, MTX/MG, HPC troubleshooting, and coding.
- Metagenome & metatranscriptome analysis
- MAGs, viruses, CAZymes, energy metabolism markers
- Functional redundancy (FRed) modeling
- Hybrid-assembly & whole-genome workflows
- Machine-learning MAG binning (GPU/CPU)
- Daily troubleshooting, R/Python tips, figures
I post short updates daily. Use the folders below to browse ↓
📚 Series
- Amplicon Week Series (6 posts)
- Applied Statistics for Microbiome Data (8 posts)
- From Laptop to HPC: Scaling Computational Biology Workflows (6 posts)
- Metagenome Analysis Series (11 posts)
- Size-Fractionated Microbiome Series (5 posts)
- Visualization Series (5 posts)
- Whole Genome Analysis Series (5 posts)
🗂 Topics
- Genomics (8 posts)
- Linux (3 posts)
- Machine learning (2 posts)
- Pangenomics (2 posts)
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Building Custom HUMAnN3 Databases with Struo2 and GTDB: A Realistic Guide from the Trenches
A comprehensive, honest guide to building custom HUMAnN3 databases using Struo2 with GTDB r220, including all the troubleshooting, workarounds, and lessons learned from 40 hours in the trenches.
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Re-working Figure 5: Visualizing Functional Redundancy (FRed) Across Bays, Seasons, and Salinity
Final version of my R-based figure for the FRed manuscript revision, including data cleaning, outlier filtering, and multi-layered ggplot styling.
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My Journey into Microbiology, the Deep Sea, and Bioinformatics
From traditional medicine to deep-sea expeditions to becoming a computational microbial ecologist — this is my story.