Software Updates

Sawfish

is a joint structural variant (SV) and copy number variant (CNV) caller for mapped HiFi sequencing reads. It discovers germline structural variants from local sequence assembly and jointly genotypes these variants across multiple samples. Sawfish additionally applies copy number segmentation on each sample's sequencing coverage levels, synchronizing structural variant breakpoints with copy number change boundaries in the process to improve classification of breakpoint-based structural variant calls, in addition to calling copy number variants.

pbccs

combines multiple subreads of the same SMRTbell molecule using a statistical model to produce one highly accurate consensus sequence, also called a HiFi read, along with base quality values. This tool powers the Circular Consensus Sequencing workflow in SMRT Link for Sequel and Sequel II platform. On Sequel IIe and Revio platforms, HiFi generation is perfomed on the instrument.

AlphaFold

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

VPT

• (Vizgen Post-processing Tool) enables users to reprocess and refine the single-cell results of MERSCOPE experiments. VPT is a command line tool that emphasizes scalable, reproducible analysis, and can be run on a workstation, a cluster, or be deployed in a cloud computing environment.

Cellpose

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.

scVelo

is a scalable toolkit for RNA velocity analysis in single cells.

Squidpy

is the scverse toolkit for scalable analysis and visualization of spatial molecular data. It builds on scanpy and anndata, providing streamlined APIs for feature extraction, spatial statistics, and interactive exploration of tissue sections together with microscopy images.

ColabFold

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

CellRank

CellRank is a modular framework to study cellular dynamics based on Markov state modeling of multi-view single-cell data.

CellRank scales to large cell numbers, is fully compatible with the scverse ecosystem, and easy to use. In the backend, it is powered by pyGPCCA (Reuter et al. (2018)).

ColabFold

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

scvi-tools

(single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.

Cell Ranger

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

gget

is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

kb-python

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.

biobambam2

tools for early stage NGS alignment file processing including fast sorting and duplicate marking.

Hail

an open-source, general-purpose, Python-based data analysis library with additional data types and methods for working with genomic data.

Snakemake

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.