Software Updates

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

HiCExplorer

is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.

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.

Canvas

a tool for calling copy number variants (CNVs) from human DNA sequencing data.

SRA Toolkit

(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Luna

is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

Tig

is an ncurses-based text-mode interface for git.

htop

is an interactive process viewer.

dcm2niix

is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.

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.

prottest3

is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT).

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

intervene

is a tool for intersection and visualization of multiple genomic region and gene sets (or lists of items).

FastQTL

a fast, flexible, user-friendly, cluster-friendly QTL mapper.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

LUMPY

a probabilistic framework for structural variant discovery.

DataLad

provides joint management of analysis code and data. This enables you to comprehensively track the exact state of any analysis inputs that produced your results — across the entire lifetime of a project, and across multiple datasets.

vg

Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:

• nodes, which are labeled by sequences and ids

• edges, which connect two nodes via either of their respective ends

• paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges