BOL: Related items

HALC: High throughput algorithm for long read error correction

Jit — Fri, 08 Jun 2018 10:47:41 -0500

HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach) HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.

Address of the bookmark: https://github.com/lanl001/halc

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

NIAB Molecular Biology/Bioinformatics Scientist/RA Openings

Thu, 13 Nov 2014 13:37:27 -0600

D. No. 1-121/1, 4th and 5th Floors, Axis Clinicals Building, Miyapur, Hyderabad, Telangana, India- 500 049

Email: admin@niab.org.in Telephones: +91 40 2304 9403 Telefax: +91 40 2304 2740
Advertisement No: 5/2014

About NIAB National Institute of Animal Biotechnology (NIAB), Hyderabad, an autonomous institute under the aegis of Department of Biotechnology, Government of India, is aimed to harness novel and emerging biotechnologies and create knowledge in the cutting edge areas for improving animal health and productivity.

Applications are invited for the following temporary research positions to work in ongoing DBTBBSRC sponsored research project entitled “Transcriptome Analysis in Indian buffalo and the Genetics of Innate Immunity” at the National Institute of Animal Biotechnology, Hyderabad.

(A) Project Scientist – Level B (One Position)

Emoluments: Rs. 15600 + GP Rs. 5400 + 30 % HRA p.m. (Total emoluments will be Rs. 49,770/-p.m. for the duration of the project)

Essential Qualification: Candidates having M.V.Sc. in Veterinary Microbiology / Veterinary Pathology / Veterinary Public Health / Ph.D. degree in Life Sciences, Biotechnology, Molecular Biology or any other related field from the recognized university are eligible to apply.

The candidate should have a good academic record and research experience as evidenced from published in standard referred journals / patents.

Desirable: Candidates having research experience in the area of tissue culture, genomics, Transcriptomics and Advanced Molecular Biology will be given preference.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

(B) Research Associate in Bioinformatics (One position)

Fellowship: Rs. 22,000 + 30 % HRA

Essential Qualification: Candidates having Ph.D. degree or M.Tech. with three years of
experience in Bioinformatics, Computational Biology, Biotechnology, Life Sciences or any other related field are eligible to apply.

Desirable: Candidate having research experience in the area of next generation sequencing (NGS) data analysis, Genome wide association studies, Genomic selection, advance genomic data analysis etc., will be given preference. The candidate should have a good academic record and research experience as evidenced from published papers in standard journals / patents.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

Project Duration: The duration of the project is Three years and the positions are co- terminus with the duration of the project. (Initial appointment will be for one year and further extension will be granted based on annual review).

Mode of submission of application: Only online applications are to be submitted through
www.niab.org.in on or before 08 December, 2014. Link for online submission of applications will be available from 10 November 2014.

Advertisement: www.niab.org.in/Notifications/Advt_5_2014/Advt_5_2014.pdf

Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Shruti Paniwala — Thu, 25 Oct 2018 06:14:55 -0500

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

Bioinformatics JRF/RA/SRF position at PANJAB UNIVERSITY

Wed, 19 Nov 2014 20:19:49 -0600

CENTRE FOR SYSTEMS BIOLOGY & BIOINFORMATICS
UIEAST, PANJAB UNIVERSITY, CHANDIGARH

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of
the project.

Essential Qualification

For Research Fellow:-

M.Sc. in Systems Biology and Bioinformatics / Life Sciences with minimum 55% marks.

Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

For Program Assistant:-

The candidate must have M.Sc./M.Tech/MCA/PGDCA in Computer Science and must be able to handle LAN, Linex. Preference will be given to the candidate having experience in
System Administration.

Emoluments

For Research Fellow Rs. 12,500/- per month (Fixed)
For Program Assistant Rs. 12,500/- per month (Fixed)

Applications should be reach on or before 19-11-2014 in the office of the undersigned.

Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

snakepipes: A toolkit based on snakemake and python for analysis of NGS data

Jit — Thu, 30 May 2019 04:06:13 -0500

snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

DNA-mapping*
ChIP-seq*
RNA-seq*
ATAC-seq*
scRNA-seq
Hi-C
Whole Genome Bisulfite Seq/WGBS

(*Also available in "allele-specific" mode)

snakePipes can be installed via conda :

'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

Bioinformatics SUB DIC (DIC)

Fri, 12 Dec 2014 21:14:57 -0600

Project Title BIOINFORMATICS SUB DIC (DIC)

Reference Number IIT/SRIC/R/DIC/2014/314, DATED 28thNovember, 2014

Temporary Position(s)

i) Junior/ Senior Project Officer (1)
ii) Junior Project Assistant (2)

Consolidated Compensation

i) Rs.16,000/- to Rs.18,000/- p.m. (depending on qualification & experience)
ii) Rs.8,000/- to Rs.10,000/- p.m. (depending on qualification & experience)

Coordinator / PI Dr. Sudip K. Ghosh, Dept of Biotechnology.

Department / Centre / School Dept of Biotechnology

Qualifications & Experience

(i) M. Sc in any branch of Life Sciences with experience in Molecular Biology/Genetics/Biochemistry preferably a Post Graduate diploma in Bioinformatics or two years working experience in bioinformatics (Minimum 60% marks starting from matriculation examination).

(ii) B. Sc. /B.A. /B. Com/Diploma in Management or Computer Science. Knowledge in computer software will be preferred (minimum 50% marks starting from matriculation examination).

More Information

Interested eligible persons may apply on plain paper, giving full bio-data along with attested copies of testimonials to the undersigned on or before 11thDecember, 2014.

Sponsor DBT, NEW DELHI

Last Date 11 Dec 2014

Application Fee Demand Draft for Rs.50/- (Not for female candidates) drawn in favour of IIT Kharagpur payable at Kharagpur

Advertisement: www.iitkgp.ac.in/topfiles/sric_job_details.php?serial=2826

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Jit — Thu, 28 May 2020 21:57:03 -0500

Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

Address of the bookmark: https://github.com/dnanexus/parliament2

Internship Program for Bioinformatics / Biotechnology / MBA / MCA (No. Of Vacancy: 5)

Mon, 15 Dec 2014 08:11:02 -0600

ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology / MBA / MCA students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis or marketing or software development. Applications are accepted throughout the year. Accepted students will be notified through email.