BOL: Related items

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/

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

Address of the bookmark: https://github.com/lh3/bfc

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

HiGlass: a tool for exploring genomic contact matrices and tracks.

Jit — Mon, 11 Jun 2018 09:44:49 -0500

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014) http://higlass.io/

Address of the bookmark: http://higlass.io/

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

LSC :a long read error correction tool

Jit — Thu, 02 Aug 2018 07:39:46 -0500

Getting Started

These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.

Read the LSC_requirements for running LSC.
Download and set-up the LSC package.
Follow the tutorial to see how LSC works on some example data.
Read the manual if anything is unclear.
You're ready, Happy LSCing!

Latest publication

Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong
Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript]
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

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

LRCstats: a tool for evaluating long reads correction methods

Aaryan Lokwani — Wed, 22 Aug 2018 11:05:04 -0500

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are longer in length than reads produced by next generation sequencing technologies, such as those produced by Illumina. However, long reads are plagued by high error rates, which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next generation sequencing technologies to correct long reads.

Address of the bookmark: https://github.com/cchauve/lrcstats

DNA Replication Process [3D Animation]

Sat, 10 May 2014 04:41:22 -0500

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/