BOL: Related items

bedtools

Jit — Fri, 24 Feb 2017 04:50:44 -0600

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

Address of the bookmark: http://bedtools.readthedocs.io/en/latest/index.html

FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads

Jit — Mon, 27 Feb 2017 09:49:45 -0600

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

Bioinformatics walk-in-interview at Tezpur University

Thu, 02 Mar 2017 04:24:46 -0600

A walk-in-interview will be held on 09 March, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University for one (01) temporary position of Junior Research Fellow (JRF) in the DBT, Govt. of India sponsored project entitled “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics” under Dr. Siddhartha Sankar Satapathy (ssankar@tezu.ernet.in), Associate Professor, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

Essential qualification: M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET.

Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science.

Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

Remuneration: Rs. 25,000/- (Rupees twenty five thousand) only + HRA as admissible per month for the 1st two years and Rs. 28,000/- (Rupees twenty eight thousand) only + HRA as admissible per month for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- (Rupees twelve thousand) only + HRA as admissible per month for the 1st two years and Rs. 14,000/- (Rupees fourteen thousand) only + HRA as admissible per month for the 3 rd year for SRF, for the candidate without NET/GATE/BET qualification. HRA will not be provided if campus accommodation is availed.

Age: Candidate shall not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ST/ OBC/Women/Differently abled.

Duration: Three (03) years or till completion of the project or until further order, whichever is earlier.

N.B. No TA/DA will be paid to the candidates for attending the interview. For further details please contact: Dr. S. S. Satapathy Associate Professor Department of Computer Science and Engineering Tezpur University, Napaam-784028 Email: ssankar@tezu.ernet.in Contact no.: +91-9435979648

More Info: www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-188-A.pdf

MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Jit — Mon, 06 Mar 2017 03:44:34 -0600

MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed an automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. Tested on both synthetic and real metagenome datasets, MetaBAT outperforms alternative methods in both accuracy and computational efficiency. Applying MetaBAT to an assembly from 1,704 human gut samples formed 1,634 genome bins (>200kb) in 3 hours, where 621 genome bins are >50% complete with <5% contamination from other species. Further analysis shows that the quality of these genome bins approaches manually curated genomes.

Address of the bookmark: https://bitbucket.org/berkeleylab/metabat

PhenoGram

Jit — Tue, 07 Mar 2017 08:35:12 -0600

With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal locations and/or regions with shapes in different colors, gene identifiers, or other text. PhenoGram also allows for creation of plots showing expanded chromosomal locations, providing a way to show results for specific chromosomal regions in greater detail.

Address of the bookmark: http://ritchielab.psu.edu/software/phenogram-downloads

Selecting between Python 2 and Python 3?

Rahul Agarwal — Wed, 10 Jul 2013 16:30:58 -0500

Which version is best for bioinformatician to work on?

sequenceserver

Jit — Fri, 10 Mar 2017 08:51:55 -0600

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

More at http://sequenceserver.com.

Address of the bookmark: https://github.com/wurmlab/sequenceserver

Research Fellow

Sat, 13 Jul 2013 11:23:20 -0500

UNIVERSITY OF CALCUTTA

A walk-in-interview will be held on 15.7.2013 at 12 noon in the Department of Biophysics, Molecular Biology and Bioinformatics, 92 A.P.C Road, Kolkata-700 009 to select one trainee research fellow and two students under DIC. The positions are purely temporary and would be for a period of six months from the date of joining which may be extended by another six months subject to successful performance.

Qualification:

For the Trainee Research Fellow: Should have a master degree in Bioinformatics or allied subjects and should have biological database development experience. Must have at least one publication.

For the Students: Should have a master degree in Bioinformatics or allied subjects and should be proficient in C-programming language. Must be familiar with techniques of Developmental Biology.

The Trainee Research Fellow would be paid a consolidated sum of Rs 10000/- per month and the students would be paid a sum amount Rs. 7000/- per month during the tenure of the project.

Advertisement:
www.caluniv.ac.in/News%20&%20Announcement/trainee_rf_DIC.pdf

Software and Tools to detect structure variation with long reads !!

Archana Malhotra — Wed, 15 Mar 2017 14:31:09 -0500

Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data.

With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:

Uncover missing heritability linked to structural variation
Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
Resolve structural variation across the complete size spectrum with basepair resolution

Following are the SV tools, which can assist you to achieve your goal.

Sniffles: Structural variation caller using third generation sequencing

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled!

More at https://github.com/fritzsedlazeck/Sniffles

MultiBreak-SV: It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.

More at https://github.com/raphael-group/multibreak-sv

Parliament: A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?

Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”

More at https://sourceforge.net/projects/parliamentsv/

https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf

PBHoney: the structural variation discovery tool

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract

More at https://sourceforge.net/projects/pb-jelly/

SMRT-SV: Structural variant and indel caller for PacBio reads

Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.

SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.

Unified variant calling user interface with built-in cluster compute support
Small indel calling (2-49 bp)
Improved inversion calling (screenInversions)
Quality metric for SV calls based on number of local assemblies supporting each call
Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
Genotyping of SVs with Illumina paired-end reads from WGS samples

More at https://github.com/EichlerLab/pacbio_variant_caller

Structural polymorphism analysis from NGS data

Sat, 13 Jul 2013 17:12:47 -0500

The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Scientific Cluster, is seeking a bioinformatician to analyze Next Generation Sequencing (NGS) data analysis. In the context of a flagship project aiming at understanding and improving the adaptive capacity of agroecosystems it will be critical to establish a link between sequence variation, functional variation, gene/protein expression and phenotypic adaptation.

The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.

Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to joets@moulon.inra.fr.