Stars
Functions for working with NCBI's Pathogen Detection data
Easily install and load packages from the tidyomics ecosystem
Aligns short reads using dynamic seed size with strobemers
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
R package for community ecologists: popular ordination methods, ecological null models & diversity analysis
Metagenomics-related extended functionalities to samtools
Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
An R package for creating a panel of diagnostic plots for residuals from a model.
✂️ ⚡ Rapid haploid variant calling and core genome alignment
A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes
The International Code of Nomenclature of Prokaryotes Described from Sequence Data
Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
Inference of putative transmission phylogenetic clusters
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Read, manipulate and visualize 'Pairwise mApping Format' data in R
An analysis and visualization platform for 'omics data
PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture