BOL: Related items

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

INTERNSHIP @ NIPGR

Sat, 13 Sep 2014 16:02:35 -0500

Applications are invited from suitable candidates for six months ‘Training Fellowship' at National Institute of Plant Genome Research (NIPGR).

About National Institute Of Plant Genome Research (NIPGR) http://www.nipgr.res.in/

The National Institute of Plant Genome Research is an autonomous institution supported by the Department of Biotechnology, Government of India. It is committed to make the institute a premier Institution for plant genomic research in the country. It was established to contribute in the achievement of such hopes as a part of national effort for meeting the challenges in the midst of fast pace of international genomic research and grasping of opportunities on long-term basis.

About the Internship:

The selected intern(s) will work in the area of in Bioinformatics under the BTISNET program of DBT in the Distributed Information Sub center (DISC) facility at NIPGR, New Delhi, under the supervision of Dr. Gitanjali Yadav, Scientist, NIPGR.

Who can apply:

Students currently pursuing the final year of Masters Degree (or equivalent) in Bioinformatics/Biotechnology with strong interest in Computational Biology and First class/division throughout academic career may apply.

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

Java utilities for Next Generation Sequencing by Pierre Lindenbaum

Robert M Willioms — Mon, 15 Sep 2014 17:24:49 -0500

Java utilities for Bioinformatics

https://github.com/lindenb/jvarkit

Address of the bookmark: https://github.com/lindenb/jvarkit

NCBI PSI-BLAST Tutorial

Fri, 23 Aug 2013 02:25:02 -0500

http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.

KAU Thrissur Biotech/Bioinformatics RA/SRF/JRF/Trainee/Studentships

Fri, 26 Sep 2014 20:07:28 -0500

Applications are invited from eligible candidates for the following posts at Bioinformatics Centre (DIC), IT- BT Complex, College of Horticulture, Kerala Agricultural University, Vellanikkara, Thrissur.

1. Research Associate
Emoluments*: 14880/- + HRA
Qualification needed: Ph.D/M.Sc in Bioinformatics or Ph.D/M.Sc in Agriculture or Biotechnology with advanced Diploma in Bioinformatics
Desirable: 2 year experience in Bioinformatics.

2 Senior Research Fellow
Emoluments*: 10230/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/ Biotechnology with Diploma in Bioinformatics.
Desirable: One year experience in Bioinformatics

3 Junior Research Fellow
Emoluments*: 9300/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/Biotechnology/Plant Sciences with Diploma in Bioinformatics.

4 .Trainee/Studentship Bioinformatics
Emoluments*: 5000/-
Qualification needed: M.Sc in Bioinformatics with good knowledge of Bioinformatics softwares and tools.

5 Trainee/ Studentship Biotechnology
Emoluments*: 5000/-
Qualification needed: M.Sc in Biotechnology, with working knowledge in tissue culture, molecular markers and cloning of genes.

Candidates with the required qualifications and experience may give an application in the prescribed format with attested copies of certificates to prove eligibility on or before 30th November 2014. The applications are to be addressed to The Associate Dean, College of Horticulture and send to "Professor & Coordinator, Bioinformatics Centre (DIC), IT-BT Complex, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680 656”. The envelope may be superscribed “Application for the post at Bioinformatics Centre”.

*Emoluments are likely to be revised in 2014-2015

More at http://www.kaubic.in/downloads/Notification_bic.pdf
http://www.kaubic.in/downloads/Application%20form.pdf

Sequence - Evolution - Function; Computational Approaches in Comparative Genomics

Jit — Sun, 06 Aug 2017 06:58:12 -0500

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK20260/

FACULTY POSITION at NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA

Sun, 05 Oct 2014 15:45:13 -0500

NIT, Rourkela, an institute of national importance under Ministry of HRD, Govt. of India invites applications from Indian nationals possessing excellent academic background along with commitment to quality teaching and research for faculty positions at the level of Professor, Associate Professor and Assistant Professor in most branches of Engineering, Science, Management and Humanities as per following table:-

1 Asst. Professor (on Pre-Ph.D. Contract)

2 Asst. Professor (on Contract)

3 Asst. Professor

4 Associate Professor

5 Professor

Life Sciences:-

i)Biochemistry and Molecular Biology; ii)Cell and Developmental Biology; iii)Immunology and Molecular Medicine; (iv) Microbiology and Ecology (v)Bioinformatics Group; vi)Biophysical Sciences

HOW TO APPLY:-

a. Candidates willing to apply for one or more posts are requested to apply online at “http://www.nitrkl.ac.in/ JOBS & TENDERS /Faculty Position” .
b. Persons employed in Government and Semi-Government organizations may apply directly against the standing advertisement. For this the application should be completed online. The printout of the application generated online should be submitted through employer if shortlisted for interview.
c. The online application can be filled in multiple sessions.
d. Candidates are required to check the Institute website from time to time for latest information, application status call for interview, change of dates and final results.
e. Applications shall be received online only. Please do not send application or CV against this advertisement by email or letter mail.

More Info: http://nitrkl.ac.in/Jobs_Tenders/1FacultyPosition/Default.aspx

Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Neel — Fri, 07 Feb 2020 07:16:22 -0600

Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.
Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
Quickly takes the user to each variant site for viewing (also available as an automated report)
Overview of assembly can help detect and fix misassemblies
Editing time reduced by the program's ability to pin-point problem areas
Editing is guided by error probabilities

Address of the bookmark: http://www.phrap.org/consed/consed.html

Tools for Sequence translation !

Abhi — Tue, 08 Nov 2022 03:37:58 -0600

BOrf - https://github.com/betsig/borf

CodAn - https://github.com/pedronachtigall/CodAn

EMBOSS-Sixpack - https://www.ebi.ac.uk/Tools/st/emboss_sixpack/

esl-translate - http://hmmer.org/, https://github.com/EddyRivasLab/easel

GeneMarkS-T - http://exon.gatech.edu/GeneMark/license_download.cgi

ORFfinder - https://www.ncbi.nlm.nih.gov/orffinder/ (web server)

PLASS - https://github.com/soedinglab/plass

Prodigal - https://github.com/hyattpd/Prodigal

TransDecoder - https://github.com/TransDecoder/TransDecoder