BOL: Related items

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

DIYA: a bacterial annotation pipeline for any genomics lab

Jit — Fri, 30 Jun 2017 08:48:26 -0500

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/Diya

Address of the bookmark: https://sourceforge.net/projects/diyg/

MeDuSa: a multi-draft based scaffolder

Abhimanyu Singh — Wed, 14 Feb 2018 02:49:00 -0600

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries.

Address of the bookmark: https://github.com/combogenomics/medusa

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

Installing Salmon for Trinity !

Rahul Nayak — Tue, 03 Jul 2018 09:02:29 -0500

➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ conda install salmon
Solving environment: done

## Package Plan ##

environment location: /home/urbe/anaconda3

added / updated specs:
- salmon

The following packages will be downloaded:

package | build
---------------------------|-----------------
boost-1.64.0 | py36_4 331 KB conda-forge
jemalloc-5.1.0 | hfc679d8_0 8.2 MB conda-forge
boost-cpp-1.64.0 | 1 17.8 MB conda-forge
salmon-0.10.2 | 1 3.7 MB bioconda
conda-4.5.5 | py36_0 624 KB conda-forge
tbb-2018_20171205 | 0 1.2 MB conda-forge
------------------------------------------------------------
Total: 31.8 MB

The following NEW packages will be INSTALLED:

boost: 1.64.0-py36_4 conda-forge
boost-cpp: 1.64.0-1 conda-forge
jemalloc: 5.1.0-hfc679d8_0 conda-forge
salmon: 0.10.2-1 bioconda
tbb: 2018_20171205-0 conda-forge

The following packages will be UPDATED:

conda: 4.5.4-py36_0 conda-forge --> 4.5.5-py36_0 conda-forge

Proceed ([y]/n)? y

Downloading and Extracting Packages
boost-1.64.0 | 331 KB | ####################################################################################################################################### | 100%
jemalloc-5.1.0 | 8.2 MB | ####################################################################################################################################### | 100%
boost-cpp-1.64.0 | 17.8 MB | ####################################################################################################################################### | 100%
salmon-0.10.2 | 3.7 MB | ####################################################################################################################################### | 100%
conda-4.5.5 | 624 KB | ####################################################################################################################################### | 100%
tbb-2018_20171205 | 1.2 MB | ####################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

AlignQC: A tool for assessing an alignment, and generating reports that are easy to share

Jit — Tue, 07 Aug 2018 04:41:07 -0500

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.

https://f1000research.com/articles/6-100/

https://github.com/jason-weirather/AlignQC

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/AlignQC/

nQuire: A statistical framework for ploidy estimation using NGS short-read data

Jit — Thu, 31 Jan 2019 05:12:19 -0600

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

https://github.com/clwgg/nQuire

Address of the bookmark: https://github.com/clwgg/nQuire

IITM-Tokyo Tech Joint Symposium

Jit — Thu, 24 Oct 2019 10:30:25 -0500

The IITM-Tokyo Tech Joint Symposium is a biannual international symposium held in Indian Institute of Technology Madras (IITM), India in collaboration with Tokyo Institute of Technology (Tokyo-Tech), Japan. During the symposium, experts in various domains of Bioinformatics gather from India and Japan under one roof to discuss and present their works. This provides an unique opportunity to the researchers and students to learn the frontiers and interact with eminent scientists in Bioinformatics. The 5th IITM - Tokyo Tech Joint Symposium titled "Current trends in Bioinformatics: Big data analysis, machine learning and drug design", will be held on 6th - 7th March 2020 in IITM, Chennai, India.

The symposium will focus on topics in the below mentioned areas.

Topics: Algorithms for biomolecular sequences / structures Bioinformatics databases and tools Protein function Structure based drug design Machine learning Deep learning Large scale data analysis Big Data NGS Analysis Protein interactions/network Molecular modelling/docking/screening Biomolecular structure and function More

Info: https://web.iitm.ac.in/bioinfo2/symposium2020/home

Industrial Training in Computer Aided Drug Designing (CADD)

RASA Life Sciences — Wed, 13 Nov 2019 05:00:44 -0600

Learn More about Computer Aided Drug Designing (CADD)!!!

#rasalsi #rasa In our Industrial program you will get Knowledge on RNA Seq, CHIP Seq,

Batch Starts From 18^th November 2019

#hurryup #registernow #enquirenow The primary goal of the industrial training program is to provide students with necessary skills making with employable. RASA LSI trains students with the enhanced skills required for them to excel in jobs in biotechnology, pharmaceuticals, BioIT and related industry sectors. At Rasa you will learn from industry leaders how to apply these skills in life science & have a command over software developing process by using various methodologies. For Registration visit us on: https://www.rasalsi.com/index.php/front-page/industrial-training/

Project Associate-I | Project Associate-II | Senior Project Associate @ IGIB

Thu, 05 Aug 2021 16:11:32 -0500

Experience in Next Generation Sequencing (NGS) application and interest in Genomics/ Clinical / Translational Applications. OR Good computational programming skills and deep interest in working on interface of Genomics and Clinical application.

Project Scientist-I
Experimental / Computation analysis experience in highthroughput genomics/ clinical application.

Project Manager
Experience in handling large biological projects involving high-throughput genomics/ clinical application.

Scientific Administrative Assistant
Lab Work.

More at https://vinodscaria.genomes.in/positionsopen