BOL: Related items

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581

HistoneDB 2.0 – with variants

Anjana — Fri, 03 Jun 2016 05:06:20 -0500

This histone database can be used to explore the diversity of histone proteins and their sequence variants in many organisms. The resource was established to better understand how sequence variation may affect functional and structural features of nucleosomes. To get started, select a histone type to explore its variants.

More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

MutaBind

Jit — Mon, 06 Jun 2016 13:34:09 -0500

MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable mutant structural model. http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

GAEMR

Jit — Tue, 14 Jun 2016 06:18:37 -0500

The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete analysis report, or executed individually to generate specific charts and tables. GAEMR standardizes input by converting a variety of read types to Binary Alignment Map (BAM) format, allowing a single input format to be entered into GAEMR’s analysis pipeline, hence enabling the generation of standard reports.

GAEMR’s analysis philosophy is centered on contiguity, correctness, and completeness -- how many pieces in an assembly composed of, how well those pieces accurately represent the genome sequenced, and how much of that genome is represented by those pieces. By performing over twenty different analyses based on these principles, GAEMR gives a clear picture of the condition of a genome assembly.

Address of the bookmark: https://www.broadinstitute.org/software/gaemr/

CovCal: Coverage / Read Count Calculator

Jit — Wed, 15 Jun 2016 18:08:13 -0500

Coverage / Read Count Calculator

Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

Instructions: set the read length/configuration and genome size, then select what you want to calculate.

Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Number of reads. Source code on GitHub.

Address of the bookmark: http://apps.bioconnector.virginia.edu/covcalc/

Mauve: a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion

Jit — Sat, 24 Dec 2016 09:20:53 -0600

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

EasyBuild

Jit — Fri, 27 Jan 2017 16:00:43 -0600

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

Amity University Bioinformatics Summer Program - Kolkata

eliabrodsky — Tue, 11 Jun 2019 21:27:10 -0500

Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

NCBI Remap

Jit — Thu, 11 Feb 2016 11:02:26 -0600

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

Easyfig

Poonam Mahapatra — Fri, 29 Apr 2016 05:49:39 -0500

Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/