Ling-Yi
@lingyi.bsky.social
🧬🦠👩🏻💻bioinformatics | machine learning | microbiology
Based on our results we are currently developing a new CNN tool with even more accurate predictions: github.com/Yasas1994/Ja... Stay tuned! (4/4)
GitHub - Yasas1994/Jaeger: Jaeger is a quick and precise pipeline for detecting phages in sequence assemblies.
Jaeger is a quick and precise pipeline for detecting phages in sequence assemblies. - Yasas1994/Jaeger
github.com
April 25, 2024 at 8:30 AM
Based on our results we are currently developing a new CNN tool with even more accurate predictions: github.com/Yasas1994/Ja... Stay tuned! (4/4)
Tools' performance ranked similarly in different biomes. #MachineLearning 🤖 tools outperformed homology-based tools. #CNN tools performed the best. The best tool was PPR-Meta, which uses a CNN containing two paths—a “base path” and a “codon path”: academic.oup.com/gigascience/.... (3/4)
PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
AbstractBackground. Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chrom
academic.oup.com
April 25, 2024 at 8:30 AM
Tools' performance ranked similarly in different biomes. #MachineLearning 🤖 tools outperformed homology-based tools. #CNN tools performed the best. The best tool was PPR-Meta, which uses a CNN containing two paths—a “base path” and a “codon path”: academic.oup.com/gigascience/.... (3/4)
We used paired viral (TP) and microbial (TN) metagenomes from #Antarctic water 🇦🇶🌊, tomato soil 🍅🌱, and human gut 💩. Real-world data 1: has high complexity, 2: avoids training/testing overlap, and 3: is more realistic than cropping mock contigs from reference genomes. (2/4)
April 25, 2024 at 8:29 AM
We used paired viral (TP) and microbial (TN) metagenomes from #Antarctic water 🇦🇶🌊, tomato soil 🍅🌱, and human gut 💩. Real-world data 1: has high complexity, 2: avoids training/testing overlap, and 3: is more realistic than cropping mock contigs from reference genomes. (2/4)