Software Updates

scvi-tools

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

Google Cloud SDK

tools and libraries for interacting with Google Cloud products and services.

Emacs

an extensible, customizable, free/libre text editor.

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

Julia

The Julia programming language is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

scvi-tools

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

Tombo

a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.

DosageConvertor

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.

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.

NanoPack

a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.

Sniffles

a structural variation caller using third generation sequencing.