BOL: Related items

pybedtools

Shruti Paniwala — Wed, 20 Aug 2014 01:03:41 -0500

pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs (https://github.com/arq5x/bedtools), which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python. See full online documentation, including installation instructions, at http://pythonhosted.org/pybedtools/.

More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/

Referee: Genome assembly quality scores

Jit — Sun, 04 Nov 2018 16:44:30 -0600

Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.

We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

Bioinformatics JRF/SRF position at IARI

Thu, 04 Sep 2014 04:14:01 -0500

DIVISION OF NEMATOLOGY
INDIAN AGRICULTURAL RESEARCH INSTITUTE
NEW DELHI 110012
Applications are invited for the posts of one Junior
Research Fellow and one RA in the DBT funded project entitled “ Plant parasitic nematode genome informatics - insilico resource development”. The project is for a period of three years.

Essential qualifications for JRF
: M. Sc. in Bioinformatics with experience in Proteomics, genomics and structural biology. Knowledge of programming language, pearl and database – HTML, CSS,php and Java script.
Essential qualifications for Research Associate:
MSc/MTech in Bioinformatics with three years experience or Ph.D in Bioinformatics with experience in proteomics, genomics and structural biology. Knowledge of programming language, perl and database
– HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm designing.
Age limit : 35 years maximum (5 year relaxation for SC/ST and women candidates)
Emoluments:
JRF: 16,000 + 30% HRA
.
Res Assoc: Rs22,000 + 30% HRA
The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.
Interested candidates
should send the duly filled application forms (format in the following page ) so as to reach on or before 20.9.2014 along with all the relevant documents.

More at http://www.iari.res.in/files/JRF_RA-03092014-20140903-135319.pdf

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

Earth BioGenome Project

Jit — Wed, 25 Apr 2018 07:48:56 -0500

The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose cells have a nucleus that houses their chromosomal DNA. To date, the genomes of less than 0.2 percent of eukaryotic species have been sequenced.

More at https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life

URDIP Pune Bioinformatics SRF/PA Openings

Sat, 20 Sep 2014 20:48:50 -0500

CSIR UNIT FOR RESEARCH AND DEVELOPMENT OF INFORMATION PRODUCTS
NCL Campus, S.No.113,114, Pashan, Pune 411 008

ADVERTISEMENT NO. - URDIP/ 5/2014

Learning opportunity for young Science and Engineering professionals to make a career in Information Science Industry CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of Scientific Informatics (ChemBioinformatics/Patent Informatics/Phytoinformatics/Toxinformatics) and related
software development projects.

Applications are invited from CSIR - UGC NET Qualified Candidates for consideration as Project Fellow (PF) and/or Senior Project Fellow (SPF) based on the experience to work on existing and new projects at CSIRURDIP.

Project Fellow

Remuneration - (Rs. 16,000.00 + 20% HRA)

M. Sc. In Biochemistry/Microbiology/Bioinformatics [Post-code A02] only with minimum of 55% marks

Senior Project Fellow

Remuneration - (Rs. 18,000.00 + 20% HRA)

M. Sc. in Biochemistry/Microbiology/Bioinformatics [Post-code A05] only with minimum of 55% marks plus two years research or relevant informatics experience

Please visit www.urdip.res.in/career.htm to apply online by 30th September, 2014.

Successful candidates who have appeared for NET exam in 2012 and 2013 are only eligible to apply.

Advertisement: http://115.112.95.114/urhr/download/Advt5_2014.pdf

Senior Bioinformatician (Assembly) Moore Aquatic Symbiosis Project Tree of Life

Sat, 02 Oct 2021 00:28:30 -0500

You will have some previous experience with genome bioinformatics or other large scale scientific data analysis, or a newly qualified graduate student with data science skills interested in DNA sequence data. While desirable, previous experience with DNA sequencing data is not strictly necessary for the position. We have a strong publication record and culture of producing open data resources and open source software development. This role requires an investigative and solution-oriented mindset and excellent communication skills to work effectively within large national and international consortia.

More at https://jobs.sanger.ac.uk/vacancy/senior-bioinformatician-assembly-moore-aquatic-symbiosis-project-tree-of-life-458923.html

Bioinformatics SVIMS Project Assistant Walk IN

Sat, 20 Sep 2014 21:02:29 -0500

SRI VENKATESWARA INSTITUTE OF MEDICAL SCIENCES
TIRUPATI, ANDHRA PRADESH, INDIA- 517 507
BIOINFORMATICS CENTRE, DEPARTMENT OF BIOINFORMATICS

Eligible candidates are invited for a walk-in-interview for recruitment of Project Assistant in SVIMS Bioinformatics centre under the BTISnet Project entitled “Creation of Bioinformatics Infrastructure Facility for promotion of Biology teaching through Bioinformatics” on 25.09.2014 at 11 AM in SVIMS, Tirupati. The engagement will be made purely on temporary basis for a period of one year and it can be terminated at any time without notice or without assigning any reason thereof by the Coordinator of the Project. The person engaged shall not be entitled for any claim implicit or explicit for absorption in the University.

1. Name of the post : Project Assistant

2. Qualification :
i) Essential : MSc Bioinformatics/MTech (Biotechnology/Bioinformatics)

ii) Desirable : Experience in Bioinformatics research work (Preference will be given to candidates qualified in BINC/UGC/CSIR/NET/GATE)

3. Remuneration : 16000 + 10% HRA for NET/GATE candidates 14000 + 10% HRA for M. Tech / M.Sc. Candidates

4. Place of posting : Tirupati

5. Duration of the Project : One year

Terms and conditions:

1. Candidates are required to submit the Biodata relevant certificates in support of their age and educational qualification etc., before the interview committee, SVIMS University, Tirupati.

2. Candidates called for interview will attend the interview at their own cost.
3. Interim enquiries will not be entertained.
4. The maximum age limit for Project Assistant is 28 years for general category and 33 years for SC and ST category candidates as on 25th September, 2014.

http://svr98.ehostpros.com/~svimsb98/Project%20Assistant_notification.pdf

The Breeding API (BrAPI) project

BioStar — Wed, 06 Jan 2021 19:51:17 -0600

The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to be used by anyone interested in plant breeding data management.

Address of the bookmark: https://brapi.org/