Stars
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
Foldseek enables fast and sensitive comparisons of large structure sets.
Bilingual Language Model for Protein Sequence and Structure
A flexible pipeline for complete analysis of bacterial genomes
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
A pairwise sequence aligner written in Rust
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
A Nextflow full-length 16S profiling pipeline for ONT reads
🚀 R package: future: Unified Parallel and Distributed Processing in R for Everyone
Nextflow pipeline for plasmid detection and classification from metagenomic data
WtP: Phage identification via nextflow and docker or singularity
Analyzing sketching and sampling approaches for fast and accurate read classification
🚥 Visualizing publication-quality multiple sequence alignment using ggplot2
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A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
A versatile pairwise aligner for genomic and spliced nucleotide sequences
All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis
💔 An implementation of scale functions for setting axis breaks of a 'gg' plot.
Software for generating Metagenomic samples of realistic Microbial Mock communities
Repository for suggesting new lineages that should be added to the current scheme