Software Updates

RSEM

(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

TensorFlow

an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.

bpp

implements a versatile high-performance version of the BPP software

ExaBayes

is a software package for Bayesian tree inference.

treePL

is a phylogenetic penalized likelihood program.

IQ-TREE

efficient and versatile phylogenomic software by maximum likelihood.

R-pkgs-Biogrids

contains common and requested R packages for BIOGRIDS. This title is dependent on R.

TBProfiler

profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data.

picard-slim

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Picard

a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.

MutMap

pipeline to identify causative mutations responsible for a phenotype. Implements bulked segregant analysis.

LiRA

(Linked Read Analysis) a computational tool for removing amplification artifacts from single-cell DNA sequencing data and estimating mutation rates in single cells.

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.

FusionCatcher

finds somatic fusion-genes in RNA-seq data.

fgbio

a set of tools to analyze genomic data with a focus on Next Generation Sequencing.

DROP

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

Cytoscape

a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

bcbio-variation

bcbio-variation is a toolkit to analyze genome variation data, built on top of the Genome Analysis Toolkit (GATK) with Clojure. It supports scoring for the Archon Genomics X PRIZE competition and is also a general framework for variant file comparison. It enables validation of variants and exploration of algorithm differences between calling methods by automating the process involved with comparing two sets of variants. For users, this integrates with the bcbio-nextgen framework to automate variant calling and validation. For developers, bcbio.variation provides command line tools and an API to clean and normalize variant data in VCF format avoiding comparison artifacts associated with different variant representations.

bcbio-nextgen

provides best-practice pipelines for automated analysis of high throughput sequencing data with the goal of being quantifiable, analyzable, scalable and reproducible. The development process is fully open and sustained by contributors from multiple institutions. Bioinformaticians, biologists and the general public should be able to run these tools on inputs ranging from research materials to clinical samples to personal genomes.

bazam

is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files.

Bazam is a smarter way to realign reads from one genome to another. If you've tried to use Picard SAMtoFASTQ or samtools bam2fq before and ended up unsatisfied with complicated, long running inefficient pipelines, bazam might be what you wanted. Bazam will output FASTQ in a form that can stream directly into common aligners such as BWA or Bowtie2, so that you can quickly and easily realign reads without extraction to any intermediate format. Bazam can target a specific region of the genome, specified as a region or a gene name if you prefer.

ASCIIGenome

a command-line genome browser running from terminal window and solely based on ASCII characters.

Juicer

a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can:

Go from raw fastq files to Hi-C maps binned at many resolutions Automatically annotate loops and contact domains with the Juicer tools Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU

Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.

PASTA

is an implementation of the PASTA (Practical Alignment using Saté and TrAnsitivity) algorithm.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.