BOL: Related items

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Jit — Tue, 15 May 2018 07:35:26 -0500

HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others. With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies, including but not limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomics Linked-Reads proximity-ligation (Hi-C) reads high-coverage sequencing (>40x coverage-per-SNP) using above technologies combinations of the above technologies (e.g. scaffold long reads with Hi-C reads) See below for specific examples of command line options and best practices for some of these technologies. NOTE: At this time HapCUT2 is for diploid organisms only. VCF input should contain diploid variants. If you use HapCUT2 in your research, please cite: Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:10.1101/gr.213462.116

Address of the bookmark: https://github.com/vibansal/HapCUT2

Savitribai Phule Pune University Recruitment for 04 JRF Post in April 2015

Mon, 27 Apr 2015 20:28:59 -0500

Savitribai Phule Pune University announced application for recruitment to the post of Junior Research Fellow. The candidates for the post can apply through prescribed format before 10 May 2015.
Description:

Important Date & Details

Closing Date for Registration: 10 May 2015

Details of Post

Name of Post: Junior Research Fellow- 04 Posts

Pay Scale: Rs. 12,000 or 16,00+ HRA Post Graduate degree with NET (16,000+HRA) Post Graduate Degree (12,000+HRA)

Eligibility Criteria: M.Sc. in Microbiology/Marine Microbiology/ Marine Biotechnology/Biotechnology/Bioinformatics/Zoology or equivalent degree with minimum 60% marks or equivalent grade

Age Limit- Not more than 28 years

Organisation Name: Savitribai Phule Pune University
Eligibility for the post:

Selection Procedure: The selection procedure is through personal interview. No TA/DA will be paid for appearing in the interview.

How to Apply: The candidates may send their application along with CV to the Head Department of Zoology, Savitribai Phule University on or before 10 May 2015.

gSearch: a fast and flexible general search tool for whole-genome sequencing

Jit — Mon, 06 Aug 2018 17:19:15 -0500

gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.

Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html

Indexcov: fast coverage quality control for whole-genome sequencing

Jit — Wed, 29 Aug 2018 09:20:46 -0500

indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license.

Address of the bookmark: https://github.com/brentp/goleft

Appointment of two traineeships and two studentships in Bioinformatics

Fri, 08 May 2015 00:24:20 -0500

Applications are invited for the appointment of two traineeships and two studentships in Bioinformatics for a period of six months sponsored by Department of Biotechnology, Government of India in the Bioinformatics Sub-DIC, Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope, Thiruvananthapuram 695 586. The required qualifications and other details are given below.

Position 1: Traineeship
Monthly fellowship (in rupee): 5,000/-
No. of vacancies: Two
Required Qualification: First Class M.Sc Bioinformatics/ Biotechnology/ Botany

Position 2: Studentship
Monthly fellowship (in rupee): 5,000/-
No. of vacancies: Two
Required Qualification: M.Phil/M.Tech Bioinformatics/ Biotechnology/ any branch of Life Science students for doing their thesis work in the area of Bioinformatics.

Age limit as on 1.1.2015, 28 years. Age relaxation will be provided for SC, ST, OBC candidates as per Govt. norms.

Interested candidates may appear for walk-in-interview on 15th May 2015 at 10.30 am at JNTBGRI, Palode, Thiruvananthapuram. The candidate should report to the Office at Palode before 10.00 am.

More at http://jntbgri.res.in/news/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics/

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Radha Agarkar — Fri, 04 Jan 2019 10:10:48 -0600

EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/.

EXCAVATOR is a novel software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.
EXCAVATOR has been published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract).

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

Narcis Fernandez-Fuentes Lab

Mon, 25 May 2015 07:30:00 -0500

Welcome to our web-site compiling all the research-related activities of the group. Our research interests relate to a number of areas within Bioinformatics. We have a long-standing interest in protein structure prediction and structure-to-function relationships. We work in the study of biomolecular interactions, modeling of protein complexes, the study and characterization of protein-protein interactions, peptide design, modeling of genetic variation, structure-based protein design and different aspects of Plant Bioinformatics. Take a look at the our databases and servers and the list of publications for more information.

More at http://www.bioinsilico.org/

mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Jit — Wed, 13 Nov 2019 22:20:19 -0600

mosdepth can output:

per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.
mean per-window depth given a window size--as would be used for CNV calling.
the mean per-region given a BED file of regions.
a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.
quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)
threshold output to indicate how many bases in each region are covered at the given thresholds.
A summary of mean depths per chromosome and within specified regions per chromosome.

Address of the bookmark: https://github.com/brentp/mosdepth

Genomic Scientist at UDSC

Thu, 28 May 2015 19:14:23 -0500

Centre for Genetic Manipulation of Crop Plants

Department of Genetics

University of Delhi South Campus

NEW DELHI – 110 021

WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT & LAB / FIELD ATTENDANT

1 Research Scientist (RS) – 3

DBT, Ph. D.

Experience on DNA Markers, plant genome mapping and bioinformatics

Salary: 60,000 (Consolidated) + 5% annual increment

Date and time: 25.06.2015 at 10:30 AM

These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.

Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.

No TA/DA will be paid for attending the interview.

www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=5492&cntnt01returnid=83

McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data

BioStar — Tue, 27 Oct 2020 00:21:18 -0500

an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae.

Address of the bookmark: https://github.com/bergmanlab/mcclintock