BOL: Related items

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

LEGE — Wed, 08 May 2024 07:32:45 -0500

ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

Address of the bookmark: https://github.com/dengzac/contig-extender

CSIR Nehru Science Postdoctoral Research Fellowship

Tue, 29 Nov 2016 12:34:59 -0600

CSIR Nehru Science Postdoctoral Research Fellowship

About Fellowship:
CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.

It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine & agriculture.

The fellowship aims at facilitating their transition from mentored to independent research career.

In addition, check these ICTS Research Fellowships:
1.) Max-Planck Partner Group Fellowships 2017-18
2.) ICTS-Simons Postdoctoral Fellowships 2017
3.) ICTS Post Doctoral Fellowships 2017
4.) Airbus Prize Postdoctoral Fellowship 2017-18

Eligibility: To be eligible for this fellowship, you:
1.) PhD degree (within 3 years of award of PhD degree), OR
2.) Those who have submitted PhD theses.
3.) Applicants should have research publications in good impact factor SCI journals.
4.) Indian nationals, Persons of Indian Origin (PIO) & Overseas Citizen of India (OCI), a can also apply.
5.) Maximum Age Limit: 32 years.

Duration:
– 2 Years.
– extendable for a maximum of 1 more year based on performance.

Remuneration:
– Rs. 50,000/- per month plus House Rent Allowance (HRA)
– A contingency grant of Rs. 3.0 lakh per annum.
– 25% of the contingency grant can be used for domestic and international travel.

Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.

How to Apply:
– Read the instructions, given at Annexure-I in this PDF file.
– And, application form is given as, Annexure-II.
– Fill the form & send it to the given address in the PDF file.

Deadline: Rolling Deadline (Applications accepted throughout the year)

Also See: Research Internship/ Fellowship in India:
1.) IIT Bombay Research Internship Awards Programme 2016-17
2.) IIT Delhi Internship Program 2016-17
3.) DAAD WISE – International Internship in Germany
4.) Summer Research Fellowship Programme| JNCASR Bangalore
5.) Indian Academy of Sciences Summer Internships 2017
6.) Winter Internship – IIT Bombay NPDE-TCA
7.) Viterbi – India Program 2017 | Research Internship in US
8.) Internship – Centre for Stem Cell Research, Vellore

Accommodation & other benefits:
– Accommodation may be provided by CSIR, if available.
– Medical benefits as per CSIR norms.

For more details:
– Check this PDF Notification of Fellowship.
– List of CSIR Labs & their work/activities can be seen at www.csir.res.in.

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction

Abhi — Mon, 08 Apr 2024 06:19:52 -0500

MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

Faculty at Indian Institute of Science Education and Research Berhampur

Mon, 19 Dec 2016 03:34:26 -0600

Advt. No: IISERBPR/DoFA/2016/2

Advertisement for Faculty Positions

The IISER Berhampur, an Institute of national importance, established through an act of Parliament is an autonomous organization under the Ministry of HRD, Govt. of India, to promote quality education and cutting edge research in basic sciences and to provide a platform for the faculty to engage in high quality education, at undergraduate and postgraduate levels. The Institute invites applications for faculty positions at the level of Assistant Professor (C) /Assistant Professor in the following disciplines:

1. Biological Sciences

2. Chemistry

3. Computer Sciences

4. Mathematics

5. Physics

Only hard copy of application in the prescribed format, via Speed Post should be sent to the Dean, Faculty Affairs, IISER Berhampur, Industrial Training Institute (ITI) Berhampur, Engineering School Road, Berhampur - 760 010, Ganjam District, Odisha, before 1700 hrs., December 30, 2016.

http://www.iiserbpr.ac.in

More Info : http://www.iiserbpr.ac.in/vacancies/Advertisement%20for%20Faculty%20Positions%20at%20IISER%20Berhampur.pdf

PRISM

Jit — Sat, 10 Dec 2016 15:19:40 -0600

PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

PRISM and PRISM_CTX were originally designed and written by Michael Brudno and Yue Jiang, The original PRISM publication can be found here.

The authors may be contacted via e-mail at: prism at cs.toronto.edu.

Additional information is available in the PRISM README file and PRISM_CTX README file.

http://compbio.cs.toronto.edu/prism/

Address of the bookmark: http://compbio.cs.toronto.edu/prism/

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation

Neel — Thu, 15 Dec 2016 05:47:35 -0600

MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de novo assemblers and contig integration software. Produces more contiguous assemblies, higher N50 values and lower number of contigs.

More at https://sourceforge.net/projects/sb2nhri/files/MyPro/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S0167701215001207

pyScaf

Bulbul — Mon, 19 Dec 2016 14:20:33 -0600

pyScaf orders contigs from genome assemblies utilising several types of information:

paired-end (PE) and/or mate-pair libraries (NGS-based mode)
long reads (NGS-based mode)
synteny to the genome of some related species (reference-based mode)

Scaffolding

In reference-based mode, pyScaf uses synteny to the genome of closely related species in order to order contigs and estimate distances between adjacent contigs.

Contigs are aligned globally (end-to-end) onto reference chromosomes, ignoring:

matches not satisfying cut-offs (--identity and --overlap)
suboptimal matches (only best match of each query to reference is kept)
and removing overlapping matches on reference.

In preliminary tests, pyScaf performed superbly on simulated heterozygous genomes based on C. parapsilosis (13 Mb; CANPA) and A. thaliana (119 Mb; ARATH) chromosomes, reconstructing correctly all chromosomes always for CANPA and nearly always for ARATH (Figures in dropbox, CANPA table, ARATH table).
Runs took ~0.5 min for CANPA on 4 CPUs and ~2 min for ARATH on 16 CPUs.

Important remarks:

Reduce your assembly before (fasta2homozygous.py) as any redundancy will likely break the synteny.
pyScaf works better with contigs than scaffolds, as scaffolds are often affected by mis-assemblies (no de novo assembler / scaffolder is perfect...), which breaks synteny.
pyScaf works very well if divergence between reference genome and assembled contigs is below 20% at nucleotide level.
pyScaf deals with large rearrangements ie. deletions, insertion, inversions, translocations. Note however, this is experimental implementation!
Consider closing gaps after scaffolding.

Address of the bookmark: https://github.com/lpryszcz/pyScaf

Postdoc at UBritishColumbia in TroutGenomics

Thu, 22 Dec 2016 08:18:46 -0600

Landscape Genomics Postdoc at UBC A research team at the University of British Columbia’s Department of Zoology and Biodiversity Research Centre is seeking a postdoctoral researcher in landscape genetics of native rainbow trout (Oncorhynchus mykiss).

This project is part of a larger Genome Canada project on genetics and physiology of adaptation to climate change in rainbow trout, and the population genomics component is in the labs of Eric Taylor and Michael Whitlock. The landscape genomics component primarily involves whole genome sequencing approaches to understanding the genomic basis of adaptation to features of habitat, but also to provide insights into phylogeography and the influence of watershed structure on population subdivision in rainbow trout. A PhD in a related field with expertise in basic theory and bioinformatic analysis of population genomics data is required.

The position is available for one year with renewal for up to three additional years. Salary is $55,000 per year plus benefits. To apply, please send a brief cover letter summarizing your qualifications for the position, a CV, and the names, addresses, phone numbers and emails of three references.

Review of applications will begin January 16, 2017. Address application materials to etaylor@zoology.ubc.ca to whom any questions can also be addressed. etaylor@zoology.ubc.ca

Mauve: a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion

Jit — Sat, 24 Dec 2016 09:20:53 -0600

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

GenomeRing: alignment visualization based on SuperGenome coordinates

Neel — Wed, 18 Jan 2017 10:24:10 -0600

The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185