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Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data
A modular graph-based Retrieval-Augmented Generation (RAG) system
Superduper: Build end-to-end AI applications and agent workflows on your existing data infrastructure and preferred tools - without migrating your data.
The open source platform for AI-native application development.
Scripts for fine-tuning Meta Llama with composable FSDP & PEFT methods to cover single/multi-node GPUs. Supports default & custom datasets for applications such as summarization and Q&A. Supporting…
Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.
mtDNA-Server 2: A web-service and Nextflow pipeline for mitochondrial genomes
Workflow for MAG quality assessment and taxonomical annotation.
assembly, binning, profiling pipelines for CAMI2
Snakemake pipeline for running Virushunter and Virusgatherer
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
software to identify primers that can distinguish genomes
SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same species) using genome synteny.
pipeline for read mapping, snp calling and annotation for bacterial genomes
Autonomous coding agent right in your IDE, capable of creating/editing files, executing commands, using the browser, and more with your permission every step of the way.
Building a Software Dev Team. Experimental Project to orchestrate a team of agents to solve programming tasks.
A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline …
Resolving Species Level Classification Using Emu