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a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs.

(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.

an ultra fast and sensitive sequence search and clustering suite

Cellpose-SAM: cell and nucleus segmentation with superhuman generalization. It can be optimized for your own data, applied in 3D, works on images with shot noise, (an)isotropic blur, undersampling, contrast inversions, regardless of channel order and object sizes.

a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.

SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

kb-python is a python package for processing single-cell RNA-sequencing. It wraps the kallisto | bustools single-cell RNA-seq command line tools in order to unify multiple processing workflows.