Jojy John

✨ December has always been my favorite month — stars, church, holidays, and joy. But this December is extra special. I’ve launched my Daily Bioinformatics Blog — Continuing in comments

🚀 𝐇𝐮𝐧𝐭𝐢𝐧𝐠 𝐕𝐢𝐫𝐮𝐬𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐌𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐞(6/6) 𝐔𝐧𝐜𝐨𝐯𝐞𝐫𝐢𝐧𝐠 𝐀𝐜𝐭𝐢𝐯𝐞 𝐕𝐢𝐫𝐚𝐥 𝐂𝐨𝐦𝐦𝐮𝐧𝐢𝐭𝐢𝐞𝐬 𝐟𝐫𝐨𝐦 𝐌𝐞𝐭𝐚𝐭𝐫𝐚𝐧𝐬𝐜𝐫𝐢𝐩𝐭𝐨𝐦𝐞𝐬 📖 Blog:jojyjohn28.github.io/blog/viromics-… 📂 Repository: github.com/jojyjohn28/met…

🧬 Our latest paper is now online! We report genomic insights into Radiobacillus sp., isolated from the Antarctic red macroalga Pyropia endiviifolia. ❄️ 220 predicted CAZymes 🌊 Potential for red algal polysaccharide degradation 🧬 Diverse PULs and plasmid-associated CAZymes

@AmitKumar_ak14 @SathyabamaS You have always been a role model to me — I still remember the “one tool per week” meetings and how much they shaped my bioinformatics journey.

Read our latest article on Antarctic seaweed associated bacteria Radiobacillus sp. genome link.springer.com/article/10.100… Only 2 known species in genus. Once upon a time PhD scholar @JojyJon, turned into a long term collaborator. Your bioinfo skills have grown, congrats 🎉 @SathyabamaS

🚀 𝐇𝐮𝐧𝐭𝐢𝐧𝐠 𝐕𝐢𝐫𝐚𝐥 𝐂𝐨𝐦𝐦𝐮𝐧𝐢𝐭𝐢𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐕𝐢𝐫𝐨𝐬𝐩𝐡𝐞𝐫𝐞 (5/6) 𝐍𝐞𝐭𝐰𝐨𝐫𝐤 𝐀𝐧𝐚𝐥𝐲𝐬𝐢𝐬 𝐰𝐢𝐭𝐡 𝐯𝐂𝐨𝐧𝐓𝐀𝐂𝐓𝟐, 𝐈𝐍𝐏𝐇𝐀𝐑𝐄𝐃, & 𝐂𝐲𝐭𝐨𝐬𝐜𝐚𝐩𝐞/𝐆𝐞𝐩𝐡𝐢 📖 jojyjohn28.github.io/blog/viromics-… 📂github.com/jojyjohn28/met… #Viralnetwork

@AmitKumar_ak14 @shilpa96752 @moesgoi @SathyabamaS @Prakash_caridea @SathyabamaSIST Wow, so cool! Let’s try to predict them. I think one of the yellow colonies could be Micrococcus or Rhodococcus, while the dark colony may be a manganese- or iron-oxidizing bacterium.

Pigmented bacterial isolates from the Bay of Bengal deep sea sediments.. @shilpa96752, JRF in @moesgoi #DOM project is working on these cool bacteria @SathyabamaS @Prakash_caridea @SathyabamaSIST

🚀 𝐇𝐮𝐧𝐭𝐢𝐧𝐠 𝐕𝐢𝐫𝐮𝐬𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐌𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐞 (4/6) 𝐖𝐡𝐨 𝐝𝐨 𝐯𝐢𝐫𝐮𝐬𝐞𝐬 𝐢𝐧𝐟𝐞𝐜𝐭? 𝐇𝐨𝐬𝐭 𝐚𝐧𝐝 𝐕𝐢𝐫𝐚𝐥 𝐋𝐢𝐟𝐞𝐬𝐭𝐲𝐥𝐞 𝐏𝐫𝐞𝐝𝐢𝐜𝐭𝐢𝐨𝐧 📖 jojyjohn28.github.io/blog/viromics-… 📂github.com/jojyjohn28/met… #Viromics #Phage #Microbiome

@raw9371 Thank you for sharing this. I will try this in the coming weeks together with my default way.

@JojyJon MetaCerberus is superior to dram-v for viruses. We find more genes and annotate more of them. And, have more databases. share.google/XESxKHas7yh8l6…

🚀 𝐇𝐮𝐧𝐭𝐢𝐧𝐠 𝐕𝐢𝐫𝐮𝐬𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐌𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐞 (3/6) 𝐖𝐡𝐚𝐭 𝐝𝐨 𝐯𝐢𝐫𝐮𝐬𝐞𝐬 𝐝𝐨? 🦠 𝐕𝐢𝐫𝐮𝐬𝐞𝐬 𝐚𝐫𝐞 𝐦𝐞𝐭𝐚𝐛𝐨𝐥𝐢𝐜 𝐞𝐧𝐠𝐢𝐧𝐞𝐞𝐫𝐬 — rewiring host metabolism. 📝 jojyjohn28.github.io/blog/viromics-… 📂github.com/jojyjohn28/met… #Viromics #Phage

🚀 𝐇𝐮𝐧𝐭𝐢𝐧𝐠 𝐕𝐢𝐫𝐮𝐬𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐌𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐞 (2/6) 🦠 𝐖𝐡𝐨 𝐚𝐫𝐞 𝐭𝐡𝐞𝐬𝐞 𝐯𝐢𝐫𝐮𝐬𝐞𝐬, 𝐚𝐧𝐝 𝐡𝐨𝐰 𝐚𝐛𝐮𝐧𝐝𝐚𝐧𝐭 𝐚𝐫𝐞 𝐭𝐡𝐞𝐲? ➡️ taxonomy ➡️ estimating abundance 📚 jojyjohn28.github.io/blog/viromics-… 📂github.com/jojyjohn28/met… #Viromics #Phage

🚀 𝐇𝐮𝐧𝐭𝐢𝐧𝐠 𝐕𝐢𝐫𝐮𝐬𝐞𝐬 𝐢𝐧 𝐭𝐡𝐞 𝐌𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐞 (1/6) A practical pipeline to identify and refine viral genomes. 📚 jojyjohn28.github.io/blog/viromics-… #Bioinformatics #Viromics #Metagenomics #Phage

You’re probably losing most of your metagenomics data. HUMAnN3 default DB ≠ environmental microbiomes. Fix: build a custom GTDB database. Result: ❌ 70% unmapped → ✅ species-resolved ecology 🧬 Day 77 jojyjohn28.github.io/blog/custom-gt…

🧬 Day 76 — Genome Coverage Coverage = total bases/genome size …but hybrid data makes it tricky I explain: ✔ 30× vs 100× ✔ Illumina vs ONT ✔ Python script for NCBI-ready output 🔗jojyjohn28.github.io/blog/genome-co… #genomics #NCBI #sequencing #Illumina #nanopore #Python

Metadata is the file that connects sequences → biology. 🧬 Day 75 — with an interactive explainer You ran QIIME 2. You have ASVs + diversity. But without metadata… You don’t know what your results mean. 📝jojyjohn28.github.io/blog/metadata-… #microbiome #QIIME2 #metadata

🧬 𝐘𝐨𝐮 𝐣𝐮𝐬𝐭 𝐚𝐬𝐬𝐞𝐦𝐛𝐥𝐞𝐝 𝐚 𝐧𝐨𝐯𝐞𝐥 𝐛𝐚𝐜𝐭𝐞𝐫𝐢𝐚𝐥 𝐠𝐞𝐧𝐨𝐦𝐞… 𝐧𝐨𝐰 𝐰𝐡𝐚𝐭? 🧬 𝐷74 𝑜𝑓 𝐷𝐵𝑓𝐽D To unlock deeper insights, you need a multi-tool annotation strategy 📝jojyjohn28.github.io/blog/genome-an… #GenomeAnnotation #PGAP #eggNOG #DRAM #InterProScan

📊 𝐅𝐫𝐨𝐦 𝐐𝐈𝐈𝐌𝐄𝟐 𝐨𝐮𝐭𝐩𝐮𝐭𝐬 → 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧-𝐪𝐮𝐚𝐥𝐢𝐭𝐲 𝐟𝐢𝐠𝐮𝐫𝐞𝐬 𝐢𝐧 𝐑 🧬 𝐷𝑎𝑦 73 𝑜𝑓 𝐷𝐵f𝐽D 👉 S𝐢𝐦𝐩𝐥𝐞, 𝐭𝐫𝐚𝐧𝐬𝐩𝐚𝐫𝐞𝐧𝐭 𝐑 𝐜𝐨𝐝𝐞 🧾jojyjohn28.github.io/blog/qiime2-to… 📦github.com/jojyjohn28/qii… #QIIME2 #RStats #DataVisualization

🧬 𝐘𝐨𝐮 𝐡𝐚𝐯𝐞 𝐚 𝐠𝐞𝐧𝐨𝐦𝐞 𝐟𝐢𝐥𝐞… 𝐛𝐮𝐭 𝐡𝐚𝐯𝐞 𝐲𝐨𝐮 𝐚𝐜𝐭𝐮𝐚𝐥𝐥𝐲 𝐬𝐞𝐞𝐧 𝐢𝐭? 🧬 𝐷𝑎𝑦 72 𝐷𝐵𝑓𝐽 A .fasta or .gbk file is just a sequence — But once visualized, it becomes an insight. 📘 jojyjohn28.github.io/blog/genome-vi… #Bioinformatics #Genome-visualization

🧬 𝐇𝐚𝐯𝐞 𝐲𝐨𝐮 𝐞𝐯𝐞𝐫 𝐛𝐞𝐞𝐧 𝐝𝐫𝐚𝐰𝐧 𝐭𝐨 𝐭𝐡𝐨𝐬𝐞 𝐛𝐞𝐚𝐮𝐭𝐢𝐟𝐮𝐥 𝐧𝐞𝐭𝐰𝐨𝐫𝐤 𝐟𝐢𝐠𝐮𝐫𝐞𝐬 𝐢𝐧 𝐩𝐚𝐩𝐞𝐫𝐬? 🧬 𝐷71 𝐷𝐵𝑓𝐽 A full guide on creating co-occurance network from genome data 📘jojyjohn28.github.io/blog/cooccurre… #NetworkAnalysis #Microbiome

Conda, Mamba, Micromamba — What's the Difference?🧬 𝐷70 𝑜𝑓 𝐷𝐵𝑓 𝐽 📘jojyjohn28.github.io/blog/conda-mam…

🧬 𝐃𝐚𝐲 𝟓 𝐨𝐟 𝟓 — 𝐅𝐫𝐨𝐦 𝐂𝐨𝐮𝐧𝐭𝐬 𝐭𝐨 𝐁𝐢𝐨𝐥𝐨𝐠𝐲 🧬 𝐷69 𝑜𝑓 𝐷𝐵𝑓 𝐽 Blog 📘: jojyjohn28.github.io/blog/day5-meta… Repo 📦: github.com/jojyjohn28/met… This wraps up the 5-part metatranscriptomics series. #Metatranscriptomics #MicrobialEcology #Bioinformatics #RNAseq

🧬 𝐃𝐚𝐲 𝟒 — 𝐑𝐞𝐚𝐝𝐬 𝐌𝐞𝐞𝐭 𝐑𝐞𝐟𝐞𝐫𝐞𝐧𝐜𝐞 🧬 𝐷68 𝑜𝑓 𝐷𝑎𝑖𝑙𝑦 𝐵𝑖𝑜𝑖𝑛𝑓𝑜𝑟𝑚𝑎𝑡𝑖𝑐𝑠 blog 📘jojyjohn28.github.io/blog/day4-meta… 📦github.com/jojyjohn28/met… A 𝐩𝐫𝐞-𝐛𝐮𝐢𝐥𝐭 𝐁𝐨𝐰𝐭𝐢𝐞𝟐 𝐢𝐧𝐝𝐞𝐱 available: 💡github.com/jojyjohn28/met… #Metatranscriptomics