Software Updates

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

ninja-nj

Nearly Infinite Neighbor Joining Application

Cell Ranger ATAC

a set of analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Single Cell ATAC data.

cellranger-arc

The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.

pixelator

A commandline tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.

biobambam2

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

STAR

(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.

dRep

a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

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.

IQ-TREE

efficient and versatile phylogenomic software by maximum likelihood.

spaln

Map and align a set of cDNA/EST or protein sequences onto a genome

allo

Multi-mapped read rescue strategy for gene regulatory analyses

Infernal

(INFERence of RNA ALignment) a program that searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

Truvari

Structural variant comparison tool for VCFs

DROP

(Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.