BOL: Related items

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

DIAMOND

Jit — Thu, 27 Apr 2017 04:21:54 -0500

DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond

Bioinformatician at 23andMe

Sat, 06 May 2017 17:57:39 -0500

23andMe’s mission is to help people access, understand, and benefit
from the human genome. We are a group of passionate individuals excited
to push the boundaries of what’s possible to help turn genetic insight
into better health and personal understanding.

Our Research Team prides itself on driving cutting edge, industrial-scale
science to make an impact that belies the team’s size, in an environment
and culture that fosters creativity, innovation, collaboration, and fun.

More than 80% of our customers consent to participate in research, and as
a result of their participation, we have one of the largest recontactable,
genotyped, and phenotyped research cohorts in the world. The scope and
breadth of our vision means that most of the methods and tools necessary
to unlock the potential of this unique resource for discovery have yet
to be developed.

Our science has garnered the respect of many members of the
broader scientific community. For a list of our publications, see
www.23andme.com/publications/for-scientists/.

Join us! Visit our Careers page (www.23andMe.com/careers) to learn more
about these open positions:

• Scientist, Research Communications
• Bioinformaticist
• Computational Biologist, Ancestry R&D
• Scientist/Senior Scientist, Statistical Genetics
• Scientist/Senior Scientist, Survey Methodology
• Scientist/Senior Scientist, Health R&D
• Senior Computational Biologist
• Biostatistician

pfontanillas@23andme.com

GWASpro: A High-Performance Genome-Wide Association Analysis Server

Rahul Nayak — Fri, 07 Dec 2018 08:04:57 -0600

GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data that may consist of up to 10 million markers and 10,000 samples from replicable lines or hybrids. GWASpro provides an interface that significantly reduces the learning curve for new GWAS investigators.

Address of the bookmark: https://bioinfo.noble.org/GWASPRO/

A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

Abhimanyu Singh — Fri, 12 May 2017 10:50:29 -0500

PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed:

ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference.

IMAGE, an iterative approach for closing gaps in assembled genomes using mate pair information. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the original assembler.

iCORN, that enables errors in the consensus sequence to be corrected by iteratively mapping reads to the current assembly. An improved version, especially correction Pacfic Bioscience assemblies (PacBio) can be found here.

RATT, a tool to transfer the annotation from a reference genome, or an earlier assembly, onto the latest assembly.

PAGIT bundles these software and makes them more accessible for users.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/pagit

PhD positions in Genova at DIBRIS - Univ. of Genoa, Italy

Thu, 18 May 2017 00:04:07 -0500

PhD positions in Genova at DIBRIS - Univ. of Genoa (Italy)

http://www.disi.unige.it/person/MasulliF/ricerca/PhDinGenova2017.html

The call for some funded positions for the 3 years PhD studies at the Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS) in Genova is available at

http://www.studenti.unige.it/postlaurea/dottorati/XXXIII/ENG/

The deadline for applications is June13, 2017 and the PhD courses and fellowships should start on Nov 2017.

Details for the application to the PhD Program in Computer Science and Systems Engineering (CODICE 6608) are at http://phd.dibris.unige.it/csse/index.php/how-to-apply

The research activity of my research group is focused on Computational Intelligence, Machine Learning, Bioinformatics, Systems Biology, and Positive Technology as described at http://www.disi.unige.it/person/MasulliF/ricerca/index.html

The research themes proposed by me and Prof. Stefano Rovetta are:

- Computational Intelligence and Machine Learning (see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T1.html)

- Computational Intelligence and Health and Wellbeing Support( see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T3.html)

You can also propose a different research theme belonging to the research activity of my group.

Looking for self-motivated PhD candidates, interested to the mathematical aspects of their research and to the development of new algorithms for intelligent data analysis, and skilled in programming and in thorough experimental data analysis. They will be part of my research group and will collaborate to our research projects and publications.

Italian and international students interested to work are invited to send their cv and the name/email-addresses of 3 referees to my email address francesco.masulli@unige.it A.S.A.P.

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Abhi — Wed, 15 May 2024 14:36:12 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

RA Bioinformatics at NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS, INDIA

Wed, 26 Jul 2017 03:49:52 -0500

NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS
(An Autonomous Institution of the Government of India)
P.O.: N.S.S., Kalyani 741251, West Bengal

Advertisement No. 137/ESTB/NIBMG/17-18

Position available Project Description: Several positions are available for the project titled: “A unified web-portal for analysis, integration and visualization of multi-omics data”. The goal of this project is to develop a user-accessible resource for integrated analysis and visualization of multi-OMICs data sets (including gene expression, genotype, methylation, microRNA, etc.). Data sets generated on various platforms shall be maintained in a stable database, accessed through standard querying mechanisms, and the results shall be displayed via user-friendly interface. The analysis engine shall run on open-source software (such as R/Bioconductor) developed in-house. All positions are contractual.

Appointment will be initially given for a period of one year which is extendable depending upon performance, availability of funds and requirements of the institute.

Project Code: 20275 Position: (No. of positions available)

Research Associate (3)

Position 1: Ph.D. or equivalent in statistics, computer science, mathematics, bioinformatics, or related subject.
Position 1: Those with experience in database management shall be preferred. Experience with UNIX or GNU/Linux operating system.
Position 1: Creation and maintenance of a database for population- and diseaseassociated variation resource. Development of programmatic interface for querying the database, filtering of the results and identification of genes of interest.

Rs. 36000/- + 10% HRA

Please apply online via web link http://apply.nibmg.ac.in/ (no other form of application will be accepted). The last date of application is 14-08-2017. All letters to attend screening test and /or interview will be sent only to the short-listed candidates by Email only. No correspondence will be made with applicants who are not shortlisted /not called for screening test and /or interview. No TA/DA will be paid for attending the screening test and /or interview.
Detail information at http://www.nibmg.ac.in/academic/Advt_20275.pdf

More Info: http://www.nibmg.ac.in/?q=Project%20Linked%20Personnel

Bioinformatics lectures !

Jit — Wed, 29 Nov 2017 05:39:54 -0600

Computational Biology is a huge field of study, that touches upon many distinct algorithmic and biological areas of study. What we are able to cover in this course will depend, in part, on the pace at which we move, which I will attempt to adjust as appropriate. However, here is a tentative list of topics I hope to cover this semester (not necessarily in order).

Optimal sequence alignment (global, local, and glocal alignment &mdash with constant & affine gap penalties
Algorithms and data structures for efficient text indexing and exact search
Heuristics for read alignment and mapping &mdash mapping DNA-seq and RNA-seq reads
Genome assembly &mdash k-mers, De Brujin graph construction and representation, long-read technology and read-overlap graph assembly
Motif finding via Gibbs sampling
Gene finding &mdash statistical models for ab initio and evidence-guided prediction of genes
RNA-seq and transcriptomics &mdash transcript assembly, abundance estimation and differential expression testing
Phylogenetics &mdash The small and large phylogeny problem; parsimony, maximum likelihood and Bayesian methods

Address of the bookmark: https://rob-p.github.io/CSE549F16/lectures/

Mesquite: A modular system for evolutionary analysis

Rahul Nayak — Tue, 18 Jul 2017 07:42:46 -0500

Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

http://mesquiteproject.wikispaces.com/

Address of the bookmark: https://github.com/MesquiteProject/MesquiteCore/releases