Software Updates

spaceranger

Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data

R

a free software environment for statistical computing and graphics.

unicycler

Unicycler is an assembly pipeline for bacterial genomes.

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.

UGENE

a free open-source bioinformatics software for macOS, and Linux.

SAIGE

SAIGE is an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks.

Julia

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

regenie

a C++ program for whole genome regression modelling of large genome-wide association studies.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

SAMtools

(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.

Cactus

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

GATK

(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.