Software Updates

HTSeq

a Python package that provides infrastructure to process data from high-throughput sequencing assays.

MACS2

(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

PyMC3

PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms. Its flexibility and extensibility make it applicable to a large suite of problems.

MapCaller

An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes.

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.

SPAdes

(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.

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.

Slingshot

an R package that provides functions for inferring continuous, branching lineage structures in low-dimensional data. Designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering, Slingshot is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

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.

Oncofuse

Oncofuse is a framework designed to estimate the oncogenic potential of de-novo discovered gene fusions. It uses several hallmark features and employs a bayesian classifier to provide the probability of a given gene fusion being a driver mutation.

GROOT

GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling). It combines variation graph representation of gene sets with an LSH indexing scheme to allow for fast classification of metagenomic reads. Subsequent hierarchical local alignment of classified reads against graph traversals facilitates accurate reconstruction of full-length gene sequences using a simple scoring scheme.

Parafly

Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.

Anvi'o

Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.

It brings together many aspects of today’s cutting-edge genomic, metagenomic, metatranscriptomic, pangenomic, and phylogenomic analysis practices to address a wide array of needs.

slclust

slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.

Fastool

Fastool is a simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them.

It makes use of the KSeq library (http://lh3lh3.users.sourceforge.net/kseq.shtml) for fast access to FastQ/A files.

rust-bio-tools

rust-bio-tools is a set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio.

Circlator

Circlator is a tool to circularize genome assemblies. The input is a genome assembly in FASTA format and corrected PacBio or nanopore reads in FASTA or FASTQ format. Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.

Pilon

Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection.

Canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. The correction phase will improve the accuracy of bases in reads.

bam2fastx

bam2fastx provides conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.