<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27323?offset=100 https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Sat, 06 Jul 2019 03:48:22 -0500 https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> Rahul Nayak https://bioinformaticsonline.com/opportunity/view/19187/srbioinformatics-analyst-ngs-at-ocimum-biosolution Sat, 15 Nov 2014 04:46:10 -0600 <![CDATA[Sr.Bioinformatics Analyst (NGS) at Ocimum Biosolution]]> “Ocimum Biosolution” is a comprehensive Integrated Life Science Informatics solutions provider with service offerings that span Sample and Data Management (LIMS, Biologics Data Management), Genomics Data Analysis Services such as Gene Expression, Genotyping, and Next Gen Sequencing, Bioinformatics and Genomics Databases (BioExpress®, ToxExpress®) and Bio-IT consulting services.

Experience Required: 3-5 years of experience

No of Positions : Multiple

Qualifications: Candidates with minimum qualification as M.Sc Bioinformatics with 3-5 years of experience in Life sciences R&D or Pharma Industry.

Ph.D candidates with research experience in Bioinformatics with publications in International journal and minimum 2 years of industry experience in clinical genomics will be preferred for this position.

Requirement:

1. Must have basic understanding of molecular biology and Genomics.

2. Experience in application development or must have expertise in programming using either of Perl/Python.

3. Experience in statistical programming using R/Bioconductor/Matlab.

4. Strong concept in statistical and mathematical modelling.

5. Experience in designing and developing the bioinformatics pipeline.

6. Must have minimum 2+ years of hands on experience in NSG data analysis such as RNA-Seq,Exome-Seq ,Chip-Seq and downstream analysis.

7. Knowledge in WGS ,WES, Targeted re-sequencing,GWAS and population genomics will be preferred.

8. Must have experience working on opensource software/Framework and commercial software for NGS data analysis and reporting.

9. Should be aware of handling big data and guiding team members on multiple projects simultaneously.

10. Should have experience coordinating with different groups of clinical research scientist for various project requirements.

11. Ability to work as team as well as independently with minimal support.

More at http://www.ocimumbio.com/careers1/

]]> https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads Fri, 31 Jan 2020 05:50:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads <![CDATA[HASLR: a tool for rapid genome assembly of long sequencing reads]]> HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. 

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> LEGE https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome Fri, 12 Dec 2014 22:27:55 -0600 https://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome <![CDATA[A 3D Map of the Human Genome]]> Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.]]> https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads Mon, 04 May 2020 02:04:03 -0500 https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads <![CDATA[HASLR: a hybrid assembler which uses both second and third generation sequencing reads]]> HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r Fri, 13 Aug 2021 07:44:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r <![CDATA[QuasR: Quantification and annotation of short reads in R]]> The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and HISAT2, through the Rhisat2 package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single R script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html

]]> Neel https://bioinformaticsonline.com/researchlabs/view/19979/zhang-lab Sun, 28 Dec 2014 12:43:08 -0600 <![CDATA[Zhang Lab]]> We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation. Please explore our website to learn more about our people and our research.

More at http://bioinfo.vanderbilt.edu/zhanglab/

]]> https://bioinformaticsonline.com/researchlabs/view/23209/bisr-jaipur Tue, 07 Jul 2015 23:12:26 -0500 <![CDATA[BISR Jaipur]]> The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:

Bioinformatics supports to researchers
Customized training in Bioinformatics for researchers and faculty members
Support in Installing, implementing and maintaining software on computer.
Create awareness for taking preventive measure against data security
Organize workshops on thrust ares of Bioinformatics
Research Training to students of Biotechnology and Bioinformatics

More at http://bioinfo.bisr.res.in/index.php

]]> https://bioinformaticsonline.com/researchlabs/view/26569/genome-stability-laboratory Mon, 07 Mar 2016 04:16:32 -0600 <![CDATA[Genome Stability Laboratory]]> The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p, MLH1p-MLH3p dependent pathway. We are interested in charactering the role of these complexes in crossover formation and distribution among all homolog pairs. Errors in this process are linked to congenital birth defects in humans such as Down's syndrome.Our laboratory is also interested in understanding the effect of genetic background on mutation rate variation using S. cerevisiae as a model. These studies are relevant for understanding cancer progression, genome evolution and architecture. We use high- throughput genomic methods as well as classical genetics to achieve these aims.

More at http://faculty.iisertvm.ac.in/~nishantkt/index.html

]]> https://bioinformaticsonline.com/researchlabs/view/26828/bioinfolab Fri, 25 Mar 2016 11:05:35 -0500 <![CDATA[BioinfoLab]]> Laboratory of Statistics and Computational tools for Bioinformatics

The Laboratory of Statistics and Computational tools for Bioinformatics (BioinfoLab) is hosted at the Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR . The laboratory has been officially opened in 2012 with the support of Programma Operativo Nazionale "Ricerca e Competitività" 2007-2013 (PON "R&C"), and it incorporates several expertise and research activities started since 2007, and supported by several CNR projects. Main interest of BioinfoLab is to develop novel statistical methods and computational tools for the analysis of high dimensional data arising from "Multi-omics" applications. In particular, current activities involve the analysis of ChIP-seq and RNA-seq experiments.

More at http://bioinfo.na.iac.cnr.it/BioinfoLab/index.html

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