Starred repositories
fastx is a Rust crate for parsing and writing FASTA/Q sequences, for learning purposes.
fastx-tools is a tool for FASTA/Q file manipulation, for learning purposes.
Learn and Practice the Rust programming language the effective way.
BioChef a tool for fast browser tests in genome and proteome.
A protocol for sequencing experiments directly in the field
A professionally curated list of awesome Conformal Prediction videos, tutorials, books, papers, PhD and MSc theses, articles and open-source libraries.
nf-mapper converts Nextflow pipelines into Mermaid gitGraph diagrams, automatically generating visual workflow maps directly from .nf source code.
Beginner, advanced, expert level Rust training material
a tool for inferring species tree from sequencing reads
Cutadapt removes adapter sequences from sequencing reads
gambit-suite / gambit
Forked from jlumpe/gambitA methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk
geNomad: Identification of mobile genetic elements
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
A list of command-line tools for manipulating structured text data
Complements Minimap2 for a fast and efficient Read-Until pipeline
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et…