BOL: Related items

Teaching Assistant at SVIMS

Fri, 31 Jul 2015 10:15:16 -0500

Eligible candidates are invited for a walk-in-interview for recruitment of Teaching Assistant in the Department of Bioinformatics on 8.08.2015 at 10 A.M. in the Committee Hall, SVIMS, Tirupati. The candidates have to attend with all original certificates of qualification, experience on the date of interview. The engagement will be made purely on adhoc basis for a period of 6 months and it can be terminated at any time without notice or without assigning any reason thereof. This is purely an adhoc appointment and the candidate will not have any right to claim permanent benefits of any kind.

1. Remuneration : Rs. 12000/- per month (consolidated)

2. Qualification : M.Sc./M.Tech. Bioinformatics (preference will be given to the candidates with BINC / NET / GATE / Bioinformatics DBT-Traineeship / Studentship and teaching experience)

3. Place of work : Department of Bioinformatics, SVIMS, Tirupati

4. No. of Position : One

Terms and conditions:

1. Candidates are required to submit the Biodata, attested copies of relevant certificates in support of their age, educational qualification, experience etc., before the interview committee, SVIMS University, Tirupati.
2. No TA / DA will be paid for attending the interview.
3. Interim enquiries will not be entertained.
4. The maximum age limit for Teaching Assistant is 34 years as on 8th August, 2015.
5. The tenure of will be further extended subject to performance of the incumbent.

Advertisement: http://svimsbic.org/Teaching_Assistant_B.I._2015.pdf

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

Interview with a bioinformatician series ...

Jitendra Narayan — Sat, 27 Dec 2014 13:30:15 -0600

The aim of this series to interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

This series will be available at BOL every fortnight.

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Rahul Nayak — Fri, 11 May 2018 05:07:45 -0500

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faster than the current PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON.

https://www.nature.com/articles/nmeth.4432

Address of the bookmark: https://github.com/xiaochuanle/MECAT

BINC examination 2015 !!!

Jitendra Narayan — Mon, 29 Dec 2014 12:23:37 -0600

Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination in 2015. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.Registration for BINC examination 2015 will open soon.

Pondicherry University Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, Pune University, Pune; Anna University, Chennai; Calcatta University (WBUT) Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; University of Kerala, Thiruvananthapuram; Jawaharlal Nehru University, New Delhi and Assam Agricultural University, Guwahati.

In the BINC 2013 examination,17 candidates were certified. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

More at http://210.212.230.224:9999/BINC/

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Jit — Mon, 28 May 2018 09:41:39 -0500

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

Address of the bookmark: https://github.com/Illumina/manta

JRF in Bioinformatics @ NEHU

Tue, 20 Jan 2015 22:57:49 -0600

Department of Botany & Bioinformatics Centre
NORTH-EASTERN HILL UNIVERSITY, SHILLONG 793022

Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (2) and Project Assistant (1) in

DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.

(i) JRF(2 nos.):

Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/Biochemistry/ Biotechnology/ Bioinformatics; Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1 no.):

Qualifications: Graduation in Science, Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

The applications through email bicnehu@gmail.com or post must reach the undersigned
within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service.

Advertisement: www.nehu.ac.in/Advertisements/BICAdvtPV_200115.pdf

nanofilt: Filtering and trimming of long read sequencing data

Jit — Mon, 30 Jul 2018 12:01:52 -0500

Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout.

Intended to be used:

directly after fastq extraction
prior to mapping
in a stream between extraction and mapping

https://github.com/wdecoster/nanofilt

Address of the bookmark: https://github.com/wdecoster/nanofilt

20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

Mon, 12 Jan 2015 01:39:45 -0600

20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)
9 - 14 August 2015 St. Augustine, Trinidad and Tobago

Organiser: Christine Carrington (University of the West Indies - UWI, St. Augustine, Trinidad and Tobago)
Co-organisers: Anne-Mieke Vandamme, Philippe Lemey (Katholieke Universiteit Leuven, Belgium), Marco Salemi, Mattia Prosperi (University of Florida, Gainesville, USA) and Karen E. Nelson (J. Craig Venter Institute, Rockville, USA)

Requests for information directly to:
Christine Carrington
Department of Preclinical Sciences
Faculty of Medical Sciences
University of the West Indies (UWI)
St. Augustine
Trinidad and Tobago
Telephone: +1-868-6452640 ext. 5009, +1-868-6848803
Fax: +1-868-6621873
E-mail: veme2015@sta.uwi.edu

Deadline for receipt of applications by local organiser: 15 March 2015
CALL FOR APPLICATIONS NOW OPEN
http://www.icgeb.org/course-application-trinidad-and-tobago-2015.html

http://rega.kuleuven.be/cev/veme-workshop/2015

NanoPack: visualizing and processing long-read sequencing data

Jit — Fri, 10 Aug 2018 18:41:34 -0500

The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

https://academic.oup.com/bioinformatics/article/34/15/2666/4934939

Address of the bookmark: https://github.com/wdecoster/nanoQC