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  • NGS in microbial diagnostics
    Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Back to overview How to use Next Generation sequencing in microbial diagnostics Next Generation sequencing NGS is a relative new technology and have provided us with a series of machines and protocols capable of changing the practice of microbiology for the diagnosis of infectious disease For instance it can be used to determine the presence of different micro organisms in clinical samples With only limited amounts of genetic material the microbial flora can be determined on species or genus levels The number of applications for NGS in microbiological diagnostics is increasing rapidly The possibilities are almost endless but there are also many pitfalls It is difficult for busy professionals working in clinical and diagnostics laboratories to keep up with the latest developments on NGS and so implementation is hindered by an inability to decide what the best technology to use is So how can this powerful data rich technology be used to provide clinically relevant information for diagnosis and treatment The number of applications for NGS in microbiological diagnostics is increasing rapidly The possibilities are almost endless but there are also many pitfalls WORKSHOP NGS IN MICROBIAL DIANGOSTICS On Wednesday September 23rd 2015 the Centre Bioscience and Diagnostics CBD from the Hogeschool Leiden together with Generade Centre of Expertise Genomics and BaseClear organises a workshop about the use of Next Generation in microbiological laboratory The course discusses how NGS can be introduced and applied in a microbiological diagnostic laboratory In addition NGS analysis will be addressed including data analysis data management and data storage The course aims at laboratory managers and managers from molecular microbiological laboratories And at persons who

    Original URL path: http://www.baseclear.com/blog/how-to-use-next-generation-sequencing-in-microbial-diagnostics_40_2.html (2016-02-12)
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  • Baseclear
    genetic research on microbial genomes and communities These technologies allow the study of functional genes and gene clusters and their influence on an organism s phenotype When microbial organisms are used in fermentation or food production genomic studies can be applied to gain improved understanding and influence their behaviour Both NIZO and BaseClear have a long history of developing microbial genetics knowledge and have in recent years specialized and invested in state of the art genomic and bioinformatics technologies The partnership offers new approaches for realizing an integrated metagenomics pipeline for efficient analyses of microbial communities which can be applied to different habitats including the gut skin or oral microbiome This solution includes detailed advice on the experimental design i e quality controls the efficient extraction of DNA a state of the art taxonomic annotation pipeline an interactive browser for the visualisation and first line interpretation of the results Further solutions will be added later this year and will include genome comparison risk assessment and functional gene content analyses The NIZO BaseClear collaboration will also work closely with customers to develop new solutions to address the most challenging issues faced in the coming years About NIZO Good food needs good science NIZO food research is a leading center in proteins bacteria and processing Our passion is to help make better foods and to be an incubator of innovation NIZO is an independent company and one of the most advanced contract research centers in the world NIZO brings the latest food technologies to life in their food grade pilot plant Customers value their gains in product quality sustainability cost effectiveness and speed to market Innovation is teamwork Only when people work together share results and continuously look for the earliest opportunity to apply results progress can be made Since 1948 NIZO

    Original URL path: http://www.baseclear.com/news/NIZO-and-BaseClear-join-forces-to-offer-state-of-the-art-microbial-genomic-solutions_80_22.html (2016-02-12)
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    Original URL path: /news/www.dtls.nl/dtl/technologypartners/hotels.html (2016-02-12)


  • Baseclear - BaseClear metaGenomics Browser
    laboratories Agro Sciences Academic Research institutes About BaseClear Our company Meet our team History Partners Distributors Why BaseClear Reasons to work with BaseClear Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Next Gen sequencing Bioinformatics Assembly and annotation Comparative genomics RNA seq analysis Microbial profiling analysis Interactive online platforms BaseTools software Sanger sequencing Microbiology Synthetic Biology BASECLEAR METAGENOMICS BROWSER multilevel taxonomic analysis across samples Our bioinformatics team has developed a perfect and unique tool to view an compare your microbial profiles and or metagenomes in an interactive manner the BaseClear metaGenome Browser BmGB BaseClear customers receive a free license valid for one year in combination with our microbial profiling or metagenomics analysis services At present the system is developed for visualization of 16S or ITS based targeted sequence analysis but will be extended also for whole metagenome analysis in the near future In brief the online portal allows interactive inspection of taxonomy tables and associated trees but also provides comprehensive overviews in pie chart and bar charts The user can specify the desired taxonomic level e g genus or species and has also the possibility to export all corresponding analysis tables and figures Finally multiple samples can be compared to detect differences between bacterial and or fungal communities The portal is accessible via https metagenomics baseclear com and supported for Firefox Internet Explorer version 9 and higher and Chrome and is a safe repository for all your metagenomes Customization of the webportal and interface is available upon request PROJECT OVERVIEW AND SAMPLE CLUSTERING Samples are clustered on the fly and displayed in a phylogenetic project overview TAXONOMIC CLASSIFICATION LIST KRONA CHART The BaseClear metaGenome Browser BmGB is designed

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/online-platforms/BmGB (2016-02-12)
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  • Baseclear - Baseclear Genome Browser
    seq analysis Microbial profiling analysis Interactive online platforms BaseTools software Sanger sequencing Microbiology Synthetic Biology BASECLEAR GENOME BROWSER the perfect tool for genome mining The BaseClear Genome Browser BGB allows customers to mine their genomes in an easy and intuitive manner It is accessible via https annotation baseclear com and supported for Firefox Internet Explorer version 9 and higher and Chrome In brief the BGB is a safe repository for genomes that are sequenced assembled and annotated at BaseClear Also we have an option to combine these genomes with other sources upon request e g NCBI GenBank files Licenses are offered for free for one year in combination with a sequencing bioinformatics project At present there are 3 distinct functions modules which all aim to get meaningful conclusions from your Next Generation sequencing data Browse and visualize Browse through your projects and samples using our comprehensive overview pages project based and taxonomy based Visualize genes and genome structures using our graphical interface The BGB provides an easy overview of of your genomes Also a graphical interface is available to view genes and genome structures Results can be exported in various formats BASIC ADVANCED AND BLAST SEARCH TOOLS Search for specific genes GC contents and many other search parameters Also a local BLAST approach is available to allow the search of particular sequences An advanced search tool allows automated queries on a number of parameters Also the customer can limit the search to specific taxa or projects The local BLAST search function gives the opportunity to BLAST a sequence of interest against one or more genomes samples projects or taxa Results can be exported in various formats COMPARATIVE GENOMICS A unique function to compare different genomes and define shared structures pan core genome or unique genes Also a mutation analysis is

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/online-platforms/BGB (2016-02-12)
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  • Baseclear - SSPACE longread
    work with BaseClear Research development Quality assurance Technologies Information News Ordering Career Jobs Internships Contact Contact details Contact form Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Next Gen sequencing Bioinformatics Assembly and annotation Comparative genomics RNA seq analysis Microbial profiling analysis Interactive online platforms BaseTools software Sanger sequencing Microbiology Synthetic Biology SSPACE LONGREAD SSPACE LongRead is a stand alone program for scaffolding pre assembled contigs using long reads e g PacBio RS reads Using the long read information contigs or scaffolds are placed in the right order and orientation in so called super scaffolds The SSPACE LongRead hybrid assembly approach has been tested on a number of bacterial genomes and in most cases results in less than 10 super scaffolds numbers based on draft assemblies constructed with one Illumina MiSeq paired end and one PacBio RS C2 SMRT library both at 100X coverage The manuscript has been accepted for publication in BMC Bioinformatics For citations refer to Boetzer M Pirovano W SSPACE LongRead scaffolding bacterial draft genomes using long read sequence information BMC Bioinformatics 2014 In principal the basic version of SSPACE LongRead is free for academics upgrades are available against a small

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread (2016-02-12)
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  • Baseclear - Direct Genomic sequencing
    Request quotation Order forms Blog Home Our services Lab Products Industries About BaseClear Blog Next Gen sequencing Bioinformatics Sanger sequencing Project sequencing Single runs 96 well plates Fragment analysis SNP and VNTR analysis Microbiology Synthetic Biology DIRECT GENOMIC SEQUENCING SERVICE Due to the optimisation of various procedures we are able to sequence directly on genomic DNA from bacteria using Sanger sequencing eliminating the need for a PCR step in the process This technique can be used for instance as gap closure tool after next generation sequencing BaseClear s Direct Genomic sequencing service Optional genomic DNA isolation Direct single Sanger sequence run on genomic DNA with a read length up to 1000 bp Maximum size of the genome is 6 MB Data analysis occurs automatically by KB caller the international standard software for superior base calling and sequence data interpretation You will receive a full report of the sequencing reaction including sequence data in FASTA SCF and ABI format No manual data editing One automatic re run of reactions that do not meet our quality standards Delivery time 1 3 working days Please note that the rate of success depends on the quality and quality of the gDNA specificity of the primer and that some parts of the genome are almost impossible to read through due to high stability regions secondary structures mispriming of the primers etc Therefore no guarantees can be given on the read length SAMPLE DELIVERY SAMPLES Bacteria should preferably be sent as pure culture on a fully grown petridish Petridishes should be sealed properly with parafilm Possible pathogenic samples should be lysed prior to sending please contact our product specialist to discuss alternative means of sample delivery Column purified gDNA in a minimal volume of 30 ul with a DNA concentration 250 ng ul DNA preferably column

    Original URL path: http://www.baseclear.com/genomics/sanger-sequencing/direct-genomic (2016-02-12)
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  • Baseclear
    PCR cloning Mutagenesis Lab Products Zymo Research Epigenetics DNA purification RNA purification Other products Sample kits Epigenetic services Bio Basic Gene Synthesis Protein expression and purification Peptide synthesis Custom antibody service Kisker Biotech Lab disposables Lab equipment Microparticles Industries Industrial Biotechnology Food Ingredients Pharma Health Water Environment Clinical Diagnostics laboratories Agro Sciences Academic Research institutes About BaseClear Our company Meet our team History Partners Distributors Why BaseClear Reasons to work

    Original URL path: http://www.baseclear.com/meet-our-team/-_10_0.html (2016-02-12)
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