BOL: Related items

RA at University of Pune

Mon, 07 Mar 2016 03:48:33 -0600

Research Associate Job vacancies in University of Pune on temporary basis

No. of Post : 01

Department : Science and Technology

Qualifications : Ph.D. with specialization in Bioinformatics/Machine Learning/ Mathematical Biology/ Computational Biology/ Systems Biology with a minimum of 55% marks in M. Sc. (50% for candidates belongs to reserved category) or equivalent grade. Candidates who have submitted their Ph.D. thesis and are waiting for award of Ph.D. are also eligible. OR M. Sc. Bioinformatics with two years of research experience in the areas mentioned above, a minimum of 55% marks in M.Sc. (50% for candidates belongs to reserved categories) or equivalent grade and at least one publication in Science Citation Index (SCI) journal. Preference will be given to B.I.N.C. /J.R.F. /N.E.T. /S.E.T. qualified candidates.

Emoluments : Rs. 20,000/- (Including H.R.A.) per month.
How to apply

The complete application along with necessary documents and certificates should reach to 'The Director, Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Caneshkhind Road. Pune - 411 007 on or before 21st March, 2016 within official hours except Sundays (i.e. 10.20 am to 06.00 pm).

More at http://collegecirculars.unipune.ac.in/sites/documents/Job%20Openings/Forms/AllItems.aspx

Gap filling or Contigs extensions tools !

Rahul Nayak — Fri, 01 Jun 2018 08:07:32 -0500

There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within paired reads" or "Toward almost closed genomes with GapFiller". There are also some tools like GAPresolution that can help to perform local re-assemblies using 454 reads. We used GAPresolution but it is not a very good software, it is useful only in some specific situations.

Take a look at the PRICE software from the DeRisi lab. Its meant to do something very similar. http://derisilab.ucsf.edu/index.php?page=software

You could also look at SSPACE (http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/), ATLAS tools (http://www.hgsc.bcm.tmc.edu/content/bcm-hgsc-software), and SCARPA (http://compbio.cs.toronto.edu/hapsembler/scarpa.html).

See the PAGIT protocol: http://www.sanger.ac.uk/resources/software/pagit/

In particular, take a look at the IMAGE tool: http://genomebiology.com/2010/11/4/R41

Also SOAPdenovo has ha function for scaffolding. Not sure about ABYSS

Here there is a useful explanation of several tools.

https://bioinformaticsonline.com/search?q=scaffolding&entity_type=object&entity_subtype=bookmarks&offset=0&search_type=entities

I could be wrong, but the above answers to your hypothetical scenario appear to miss the point that you aren't interested in assembling the full genome, just the 100 kb part you're interested in. I suggest the following algorithm:

1. Start with the initial assembly C0 of the contigs you have identified as overlapping your region of interest, and the set S of reads those contigs contain. Let C = C0.

2. Repeat:
a. Identify paired-end reads (not in C) for which one or both ends align within, or extending, contigs in C.
b. Identify unpaired reads that align extending these new paired-end reads.
c. Construct a new assembly C' from C and the new reads identified in (a) and (b).
d. Trim C' so it does not extend more than 100 kb to either end of C0. Set C = C'.
e. Let S' denote the reads that contribute to C'. If S' does not contain any reads not present in S, stop. Otherwise, Set S = S'.

3. If you don't have a complete assembly of the region of interest, generate an STS for each end of each contig, probe a library for clones including these STSes, subclone these clones into a paired-end sequencing vector, and generate paired-end reads for this library; then try steps (1) and (2) again, adding these new sequencing reads to what you had before.

4. If your average sequencing depth for the region of interest exceeds 25 or so without filling all gaps, it is likely that the remaining gaps represent sequences that are not getting cloned in your sequencing vectors. Try different sequencing vectors.

Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.

BioStar — Thu, 09 Apr 2020 04:56:09 -0500

Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly, taxonomic and functional classification, genome binning, and gene assignment. We aim to deliver the analytical framework as a robust and reliable containerized workflow system, which will be free from dependency, installation, and execution problems typically associated with other open-source bioinformatics solutions. This will maximize the transparency, data provenance (i.e., the process of tracing the origins of data and its movement through the workflow), and reproducibility.

More at https://dahak-metagenomics.github.io/dahak/

Address of the bookmark: https://github.com/dahak-metagenomics/dahak

Bioinformatics tools for telomere to telomere assembly !

BioStar — Tue, 17 Aug 2021 13:17:09 -0500

● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)
● PanGenie – algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)
● SQANTI3 – an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Rocío Amorín de Hegedüs @rocioadh)
● tama (Transcriptome Annotation by Modular Algorithms) – software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo @GenomeRIK)
● pbaa (PacBio Amplicon Analysis) – separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg @zevkronenberg)
● bellerophon – analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng @Yuanyuan929)
● svpack – tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)
● JumboDB – tool for de Bruijn graph construction (Anton Bankevich @AntonBankevich)
● uLTRA – tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin @krsahlin)
● LeafGo – workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini @ermini_luca)

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/

Project Fellow Bioinformatics at Central University of Himachal Pradesh

Tue, 09 Feb 2016 03:58:00 -0600

Project Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics)

Location : Kulu

Last Date : 07 Mar 2016

Hiring Process : Face to Face Interview
Central University of Himachal Pradesh

Project Fellow Bioinformatics Job in Central University of Himachal Pradesh

Project (MRP) entitled: “A project proposal on targeting novel prokaryotic ubiquitin like post-translational modification pathway for therapeutic interventions against Mycobacterium tuberculosis” (No. MRP-MAJOR-MICR-2013-26840)

Essential Qualification: 1. Master degree in Bioinformatics/Biochemistry/Biotechnology/Environmental Science/Microbiology or any branch of Life Sciences with a minimum of 55% marks for general category (50% in case of SC/ST/PH) 2. UGC/CSIR NET, GATE qualified candidates will be given preference. Desirable Qualification: Experience in basic Bioinformatics and Molecular Biology techniques.

Age: Below 40 years as on 01/10/2015.

No.of Post: 1

Salary: NET/GATE qualified candidate: Rs. 16,000/-p.m. for initial two years and Rs. 18,000/- p.m. for the third year. Non-NET/GATE candidates: Rs. 14,000/-p.m. for initial two years and Rs. 16,000/-p.m. for the third year.

Mode of Selection: The selection shall be made on the basis of merit. The eligible candidates are required to appear for interview before the duly constituted Selection Committee for the purpose. The scheduled date, time and venue for the interview shall be intimated to the eligible candidates through phone/ e-mail.
How to apply

Last date for the receipt of applications is 07.03.2016.

More at http://www.cuhimachal.ac.in/news_all.aspx

Des Higgins: Visualizing Multiple Sequence Alignments

Wed, 26 Feb 2014 00:50:08 -0600

Copyright Broad Institute, 2013. All rights reserved. Des Higgins (http://www.bioinf.ucd.ie) gives a very entertaining introduction to the visualization of multiple sequence alignment, and to his widely-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of sequences, and presents several approaches to this challenge, including faster algorithms and abstract views of clusters of alignments. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO. For information about data visualization efforts at the Broad Institute, please visit: http://www.broadinstitute.org/node/1363/

Centurion

Jit — Fri, 12 Feb 2016 04:45:41 -0600

Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been re-purposed for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples, and inference of centromere locations. We describe a method, Centurion, that jointly infers the locations of all centromeres in a single yeast genome by exploiting the centromeres’ tendency to cluster in 3D space. We first demonstrate the accuracy of Centurion in identifying known centromere locations from high coverage Hi-C data of budding yeast and a human malaria parasite. We then use two metagenomic samples with relatively low coverage Hi-C data to infer centromere locations for each chromosome in 14 different yeast species. For yeasts with large centromeres (e.g., S. pombe) Centurion predicts the exact centromere locations. For seven yeasts with point centromeres, Centurion predicts most of the centromeres at an average of 5~kb distance from their known locations. Finally, we predict centromere coordinates for six yeast species that currently lack centromere annotations. These results suggest that Centurion can be used for centromere identification for a large number of yeast species, even with a limited amount of Hi-C sequencing.

Paper:http://www.ncbi.nlm.nih.gov/pubmed/25940625

More at http://cbio.ensmp.fr/centurion/

Address of the bookmark: http://cbio.ensmp.fr/centurion/

PhyloGrapher - Graph Visualization Tool

Jit — Wed, 07 Mar 2018 18:11:25 -0600

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

Radka Reifová Lab

Mon, 15 Feb 2016 06:00:48 -0600

We are generally interested in the mechanisms of species origin from a molecular and ecological perspective. Particularly, we are interested in the role of sex chromosomes in speciation. Most of our research is done on birds and mammals. Currently, we focus our research on two hybridizing song birds, the Common nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia). Combining population genomic and ecological approaches we try to elucidate the genetic architecture of reproductive isolation and understand the role of interspecific competition and song convergence in the evolution of reproductive isolation between the species.

More at http://web.natur.cuni.cz/~radkas/index.php?page=research

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/