BOL: Related items

PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens

LEGE — Wed, 21 Feb 2024 06:15:13 -0600

What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

Address of the bookmark: https://github.com/lmcai/PhyloHerb/

NRCO Vacancies For Junior Research Fellow – Pakyong, Sikkim

Thu, 28 May 2015 19:10:07 -0500

Junior Research Fellow
Pay Scale:Rs 25,000/-
Educational Requirements:MSc (with NET qualification) / M.Tech degree (with or without NET) with minimum 55% marks in Biotechnology/ Bioinformatics/ Molecular Biology or any other related field.
Other Qualification:Computer Skills (Linux, Perl, Java, MySQL) with experience in advanced molecular Biology techniques.
No of Post: 01
How To Apply: Walk-in-Interviews will be held at ICAR-National Research Centre for Orchids,Pakyong 737106, Sikkim for the post of 01 (One) Junior Research Fellow and 01 (One) Project Attendant under Project ‘DBT’s Twinning programme for the NE’ titled “Assessment of chemical and genetic divergence of some fragrant orchids of north-east India for sustainable improvement of community livelihood” as indicated below. The appointment will be on contractual basis and the incumbents shall not have any claim for regular appointment in ICAR.

Details will be available at: http://nrcorchids.nic.in/Employments/Vacancy%20-%20JRF.pdf

Omega2: metagenome assembly pipeline

Jit — Mon, 10 Jul 2017 05:56:07 -0500

Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information. In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega provided comparable overall performance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison with Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a fraction of the computing time of existing overlap-layout-consensus assemblers. This indicates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for metagenomic datasets.

Address of the bookmark: http://omega.omicsbio.org/

Nicolas Corradi Lab

Tue, 26 May 2015 16:19:02 -0500

The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.
To achieve this goal, our team combines the power of next generation DNA sequencing and bioinformatics with molecular biology and experimental procedures.

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Jit — Wed, 06 Dec 2017 01:05:21 -0600

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not require restriction enzyme such as DNase Hi-C. In practice, HiC-Pro can be used to process dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data.

http://nservant.github.io/HiC-Pro/

Address of the bookmark: http://nservant.github.io/HiC-Pro/

Assistant Professor, Central University of Himachal Pradesh, India

Thu, 28 May 2015 19:22:49 -0500

Central University of Himachal Pradesh

PO Box: 21

DHARAMSHALA, DISTRICT KANGRA, HIMACHAL PRADESH – 176215

EMPLOYMENT NOTICE NO.: 02 / 2015

APPOINTMENT TO VARIOUS TEACHING, NON-TEACHING AND OTHER ACADEMIC STAFF POSITIONS

Applications in the prescribed form are invited from the eligible candidates for the following Teaching, Non-Teaching and other Academic Staff positions to be filled up on regular basis: Details of teaching positions:

15. School of Life Sciences

Computational Biology & Bioinformatics

1 (ST - 1) 2 (UR - 2)

Last Date of receipt of applications: 22ND JUNE, 2015

http://www.cuhimachal.ac.in/download/2015/may-2015/emp-notice-eng/1.%20Employment%20Notice%20No.%2002-2015%20dated%2019.05.2015_for%20Website.pdf

MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites

Neel — Mon, 05 Nov 2018 08:12:45 -0600

An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Address of the bookmark: https://github.com/olarerin/metaPlotR

RECRUITMENT FOR 6 POSITIONS OF JRF (Junior Research Fellow)

Thu, 04 Jun 2015 15:22:54 -0500

Institute of Bioresources and Sustainable Development (IBSD), a National Institute of the Department of Biotechnology, Government of India invites applications for 6 positions of JRF for 2015. The main mandate of IBSD is Conservation and Sustainable Utilization of Bioresources for the Socio-economic Development of the North East Region of India, which is a genetic treasure trove of plants, animals and microbial resources. This region falls among the World’s top 10 Biodiversity Hotspots. The broad areas of research are in Plant Bioresources, Microbial Resources, Natural Product Chemistry, Animal Bioresources and Bioinformatics and Database Management.

Minimum qualifications: M.Sc. with minimum 55% for general and OBD Category (55% for SC/St/PH) in the above-mentioned subject areas (viz. Biotechnology, Life Sciences, Microbiology, Botany, Plant Sciences, Chemistry, Zoology, Animal Sciences, Fishery Sciences and any other relevant branches).

Preference will be given to those holding valid CSIR-UGC NET JRF. DBT-JRF, ICAR-JRF, ICMR-JRF and DST-INSPIRE Fellowship while NET/SLET/SET qualified and GATE qualified candidates (90 or above percentile) are also encouraged to apply. Reservations of seats: 15% for SC, 7.5% for ST, 27% for OBC (noncreamy layer) and 3% for Physically Handicapped as per statutory norms.

Selection Procedure: If the number of JRF and INSPIRE qualified candidates is more, selection will be based on interview of the JRF and INSPIRE qualified candidates only. The selected candidates may be registered for Ph.D. in any of the recognized Universities in India.

Application Procedure: Application should be sent in the prescribed application form (available on the IBSD website). The candidate should send the completed and signed form along with self attested copies of all supporting certificates and marksheets along with an application fee of Rs.300/- (For GEN/OBC/PH) & Rs.150/- for (SC/ST), for which a Demand Draft in favour of ‘Institute of Bioresources and Sustainable Development, payable at Imphal, Manipur, should be attached with the application form. Candidates are advised to provide their email ID and mobile number as they would be contacted electronically by the Institute. Duly filled applications (with ‘Application for IBSD PhD Programme’ super scribed on the envelope) should be sent to ‘The Director, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal-795001, Manipur so as to reach on or before 6th of July, 2015. Applications send by email with scan copy of required enclosures will also be accepted and can be sent to director.ibsd@nic.in. However, in such instances, the application will be processed only after the receipt of the mailed hard copies.

Advertisement: http://ibsd.gov.in/jobs/phd_2015/IBSD_JRF_2015.pdf

Application Form : http://ibsd.gov.in/jobs/phd_2015/APPLICATION_FORM.pdf

TRITEX sequence assembly pipeline for Triticeae genomes

Jit — Tue, 20 Aug 2019 09:47:14 -0500

The pipeline is open-source and hosted in a public Bitbucket repository.

TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.

A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Rosalind Problem Solution with Perl

Jit — Tue, 09 Jun 2015 23:35:18 -0500

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...