January 2019 Newsletter
Our January update includes 25 new software titles. This brings the number of available titles in BioGrids to 208. In addition, there are over 1,500 packages and modules available for R, python and perl. Three new workshops and classes are available on the Harvard Longwood campus this month. Details on how to download the BioGrids Software Installer and get started today are given below.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: firstname.lastname@example.org.
Tracer is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Version: 1.7.1
BGT is a compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples. Version: 1.0
vcfanno allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. Version: 0.3.1
GToTree is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees. Version: 1.0.2
ProSolo is a variant caller for single cell data from whole genome amplification with multiple displacement amplification (MDA). Version: 0.6.1
bazam is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files Version: 1.0.1
kma implements a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. Version: 1.1.7
Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. Version: 2.15
yacrd is a simple and easy to use long read error-correction tool which can detect and remove chimeras. Version: 0.4.1
Fastcov is an implementation of a new algorithm, named Fastcov, to identify multiple correlated changes in biological sequences using an independent pair model followed by a tandem model of site-residue elements based on inter-restriction thinking. Version: 1.0.3
SeqKit is a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. Version: 0.10.0
TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. Version: 0.3.0
andi estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Version: 0.12
Mash is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads. Version: 2.1
FAMSA implements an algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM). Version: 1.2.5
Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. Version: 1.0.4
trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. Version: 1.4.1
Prodigal is a fast, reliable protein-coding gene prediction for prokaryotic genomes. Version: 2.6.3
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Version: 3.2.1
Pillow is the friendly PIL (Python Imaging Library) fork by Alex Clark and Contributors. The Python Imaging Library adds image processing capabilities to your Python interpreter. Version: 5.4.1
ReportLab is the time-proven, ultra-robust open-source engine for creating complex, data-driven PDF documents and custom vector graphics. Version: 3.5.12
MMTF-python is the macromolecular transmission format (MMTF) binary encoding of biological structures. This title holds the Python API encoding and decoding libraries. Version: 1.1.2
SpliceV provides analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. Version: 20190108
LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering. Version: 22.214.171.124
MultiQC aggregates results from bioinformatics analyses across many samples into a single report. Version: 1.7
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download and activate using the link button above.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide over 200 titles in five categories and an additional 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids
Training sessions available to HMS trainees:
Registration for HMS Research Computing's User Training Spring 2019 courses will open on Wednesday, January 30 at 1p. Space is limited, and registrations are first-come, first-served, available here:
Registration for the MATLAB Image Processing 2 day workshop (from MathWorks, with a $500 fee) is open now, and space is filling up fast!
The Harvard Chan Bioinformatics Core
For HSCI and on-quad HMS researchers:
Introduction to the command line interface (Shell, Unix, Linux) January 17th 1 day
Introduction to R January 28th & 29th 1.5 days
For all researchers at Harvard University and affiliated institutions:
Introduction to R January 10th 1 PM Kresge (HSPH), room 502
Need help getting software installed on new machines? Have you been planning to try Amazon Web Services (AWS) cloud computing?
BioGrids can help you get started. We have expertise in bioinformatics, programming, workflow development and high performance computing.
We improve the collection with feedback from the community.
Want to see a new application in BioGrids?
Let us know: email@example.com
BioGrids is supported by the HMS TnT fund and based upon SBGrid.org