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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.

A tool to compress FASTQ files with ultra-high compression ratio and high speed. repaq supports compressing the FASTQ to .rfq or .rfq.xz formats. Compressing to .rfq is ultra fast, while compressing to .rfq.xz provides very high compression ratio.

dysgu (pronounced duss-key) is a set of command line tools and python-API, for calling structural variants using paired-end or long read sequencing data.