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. Scroll down for the latest posts ↓
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Visualizing Genome Assemblies with Bandage: Building from Source on Linux
A practical guide to installing Bandage from source using Qt and visualizing assembly graphs generated by Flye and Shovill.
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Exploring the Pan-Genome with panX: A Practical Workflow for DARPA Isolates
A complete walkthrough using panX to analyze the pan-genome of 20 DARPA isolates—annotation, pipeline execution, interactive visualization, and core/pan gene extraction.
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Cleaning and Preparing Genomes for NCBI Submission — A Complete Workflow
Step-by-step guide for fixing adapter contamination, removing unwanted contigs, renaming FASTA headers, renumbering contigs, and preparing high-quality genomes for NCBI submission.
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Installing & Setting Up My New Linux Laptop: A Real Journey Through Dual-Boot, Partitions & Persistence
A complete walkthrough of dual-booting Ubuntu with Windows on a modern Dell NVMe laptop — from partition problems to corrupted USB drives and manual GParted rescue.
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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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Machine-learning MAG binning with SemiBin2 and Snakemake (soil metagenomes)
How I used SemiBin2 and a Snakemake workflow to recover high-quality MAGs from fragmented, high-diversity soil metagenomes.
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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.