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

Phylogenomics/Phylogenetic website

Aaryan Lokwani — Mon, 07 Apr 2014 02:17:18 -0500

Welcome to phylobabble.org, a discussion forum for phylogenetic theory and applications. The primary goal of this forum is to discuss best practice and new developments in phylogenetics. Although we do have a Troubleshooting category for getting feedback on analyses, this is not a help site for running phylogenetics programs.

A great place to chat about phylogenetics for researchers and the broader community of students and science-interested citizens.

Address of the bookmark: http://phylobabble.org/

mutatrix: a population genome simulator which generates simulated genomes.

Jit — Tue, 28 Jan 2020 04:06:58 -0600

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

More at https://github.com/ekg/mutatrix

./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

Address of the bookmark: https://github.com/ekg/mutatrix

SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

Neel — Sun, 22 Dec 2019 03:48:28 -0600

Call sviper

~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants

This will output a polished_variants.vcf file, that contains all the refined variants.

Sometimes it is helpful to look at the polished sequence, e.g. with the IGV browser. In that case you want SViper to output the polished and aligned sequences in a bam file via the option --output-polished-bam:

~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants --output-polished-bam

Address of the bookmark: https://github.com/smehringer/SViper

BioCodes/BioScripts

Jit — Tue, 22 Apr 2014 20:53:33 -0500

Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts.

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

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

RA at ALAGAPPA UNIVERSITY

Sun, 04 May 2014 23:33:15 -0500

DEPARTMENT OF BIOTECHNOLOGY
(UGC SAP and DST-FIST & PURSE Sponsored Department)
ALAGAPPA UNIVERSITY
(A State University Accredited by NAAC with „A‟ Grade)
Karaikudi - 630 004, India

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Jit — Sat, 25 Jan 2020 13:28:09 -0600

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

https://www.biorxiv.org/content/10.1101/092890v6

Address of the bookmark: https://github.com/google/deepvariant

Associate Professor - Bio-Informatics at University of Allahabad in Allahabad

Wed, 07 May 2014 00:26:53 -0500

No of vacancies: 01

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges

Shruti Paniwala — Sat, 02 Jul 2022 11:41:53 -0500

This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.

Address of the bookmark: https://github.com/mkirsche/Jasmine