BOL: Related items

Genobuntu: Package for Next Generation Sequencing and Genome Assembly

BioStar — Mon, 18 May 2020 16:47:56 -0500

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

Velvet
MiB
SSAKE
EULER
VCAKE
ABySS
ALLPATHS
Celera
SHARCGS
Allpaths
IDBA
TAIPAN
Edena
SOAPdenovo
Maq
IDBA-UD
No. of Reads present in the Ref. Seq.
ART NGS Reads Simulator
HiTEC, FASTQC
Minimum Description Length
SOAPaligner
Sequencing Read Archive Toolkit

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

A comprehensive atlas of human gene activity released !!!

Abhimanyu Singh — Tue, 02 Sep 2014 14:20:24 -0500

A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

We are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles. This is a major advance that will greatly increase our ability to understand the causes of disease across the body.

The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.

Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches” — called “promoters” and “enhancers” — are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.

Referene : www.kurzweilai.net/first-comprehensive-atlas-of-human-gene-activity-released

MitoFinder

Neel — Tue, 29 Aug 2023 02:13:01 -0500

Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link)

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

Which of the following programming language is best for a bioinformatics beginner?

Manisha Mishra — Thu, 04 Sep 2014 07:51:16 -0500

I will be doing NGS in the course of my research work and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Recommendations welcomed. Which languages would you recommend to a student wishing to enter the world of bioinformatics?

Reference Sequence Resource!

LEGE — Wed, 15 Sep 2021 21:15:22 -0500

The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability. Drosophia melanogaster experiments are mapped to either dm3 or dm6 and Caenorhabdilis elegans experiments are mapped to ce10 or ce11. T

Address of the bookmark: https://www.encodeproject.org/data-standards/reference-sequences/

Research Scientist – Bioinformatics at Sidra Medical and Research Center

Wed, 10 Sep 2014 14:35:35 -0500

Sidra Medical and Research Center(Doha, Qatar) is looking for talented Research Scientists (Bioinformatics / NGS Data Analysis).

Research Scientists within the Bioinformatics Program are involved in research related to cutting edge genomics and analysis of omics data. The research will utilize concepts, theories and best practices obtained from bioinformatics discipline and applied to biological and other biomedical data for analysis. The role may also involve designing databases, algorithm and/or computation methods for analyzing genomics and other omics data. The scientist will be working closely with the Translational Medicine Program within a state-of-the art research setting.

Please check the details of the opening and apply here: http://careers.sidra.org/sidra/Vacan...acancyID=60181

UniqueKmer: Generate unique KMERs for every contig in a FASTA file

Abhi — Fri, 17 Dec 2021 00:08:15 -0600

Generate unique k-mers for every contig in a FASTA file.

Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands).

This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers for each contig.

The output unique k-mer file and Genome file can be used for fastv: https://github.com/OpenGene/fastv, which is an ultra-fast tool to identify and visualize microbial sequences from sequencing data.

https://github.com/OpenGene/UniqueKMER

Address of the bookmark: https://github.com/OpenGene/UniqueKMER

INTERNSHIP @ NIPGR

Sat, 13 Sep 2014 16:02:35 -0500

Applications are invited from suitable candidates for six months ‘Training Fellowship' at National Institute of Plant Genome Research (NIPGR).

About National Institute Of Plant Genome Research (NIPGR) http://www.nipgr.res.in/

The National Institute of Plant Genome Research is an autonomous institution supported by the Department of Biotechnology, Government of India. It is committed to make the institute a premier Institution for plant genomic research in the country. It was established to contribute in the achievement of such hopes as a part of national effort for meeting the challenges in the midst of fast pace of international genomic research and grasping of opportunities on long-term basis.

About the Internship:

The selected intern(s) will work in the area of in Bioinformatics under the BTISNET program of DBT in the Distributed Information Sub center (DISC) facility at NIPGR, New Delhi, under the supervision of Dr. Gitanjali Yadav, Scientist, NIPGR.

Who can apply:

Students currently pursuing the final year of Masters Degree (or equivalent) in Bioinformatics/Biotechnology with strong interest in Computational Biology and First class/division throughout academic career may apply.

KAST

Neel — Wed, 23 Feb 2022 08:28:36 -0600

Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

Address of the bookmark: https://github.com/martinjvickers/KAST

Joao Pedro de Magalhaes Lab

Fri, 26 Sep 2014 19:08:34 -0500

Ageing has a profound impact on human society and modern medicine, yet it remains a major puzzle of biology. The goal of my work is to help understand the genetic, cellular, and molecular mechanisms of ageing. In the long term, I would like my work to help ameliorate age-related diseases and preserve health. No other biomedical field has so much potential to improve human health as research on the basic mechanisms of ageing. Please see our lab website for further details about our work and publications.

Functional and Comparative Genomics

http://jp.senescence.info/
http://www.senescence.info/
http://www.liv.ac.uk/integrative-biology/staff/joao-de-magalhaes/