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  • Baseclear
    quality solutions for the last 20 years BaseClear distinguishes itself by having a highly customer orientated approach working in close collaboration with customers to develop solutions specifically matched to their needs BaseClear offers a number of service packages based on the innovative Next Generation sequencing technologies Using a combination of Illumina s HiSeq2500 system and the PacBio platform offer the possibility to sequence genomes and transcriptomes more accurately than ever before Additionally over the last two decades we have gained considerable experience and expertise in microbial genome and transcriptome analysis and currently offer a comprehensive package of services to customers in these fields We are currently looking for candidates for the position of Bioinformatician m f Function The candidate will be responsible for data management and analysis of genome and transcriptome sequencing Next Generation sequencing projects Further he she will work on development and optimisation of bioinformatics analysis software and pipelines with a view to offering them as commercial services and therefore keep up to date with the newest developments in the market Also will he she work on other internal projects such as the development of the internal LIMS system and automation of analysis for the Microbiology Sequencing and Molecular Biology departments Eventually development of graphical web applications will be requested He she will work as part of a highly motivated team of scientists and technicians We are looking for A result orientated enthusiastic candidate with at least 2 years work experience in the field of bioinformatics An excellent knowledge of at least two programming languages preferably Perl Python R C sharp and in depth knowledge of Next Generation sequencing technologies are essential Additionally we are looking for a candidate who has a commercial attitude with excellent communication and presentation skills and a high level of energy and ambition

    Original URL path: http://www.baseclear.com/career-jobs/Bioinformatician-%28m/f%29_30_11.html (2016-02-12)
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  • Baseclear
    dat gespecialiseerd is in DNA analyses Wij hebben ca 50 medewerkers en zijn gevestigd op het BioSciencePark in Leiden In ruim 20 jaar tijd hebben wij met veel plezier en door hard werken een grote internationale klantenkring opgebouwd BaseClear voert een breed assortiment aan routinematige DNA testen Onze opdrachtgevers zijn onder meer te vinden in het bedrijfsleven de klinische en farmaceutische markt universiteiten en onderzoeksinstellingen BaseClear is ISO17025 geaccrediteerd sinds 2006 voor haar forensische activiteiten Voor onze groeiende Sanger sequencing Microbiologie en Molbio afdeling willen wij graag in contact komen met enthousiaste en gemotiveerde kandidaten voor de functie van Moleculair Biologisch Analist m v Sanger Micro MolBio afdeling Over de functie Als moleculair biologisch analist ben je betrokken bij de dagelijkse praktische uitvoer van moleculair biologische werkzaamheden binnen de Sanger sequencing Microbiologie en MolBio afdeling Je maakt onderdeel uit van een gemotiveerd team van managers en senior analisten De werkzaamheden zijn ondermeer ontvangst en inschrijven van klant projecten zuiveren van DNA samples inzetten en zuiveren van sequencing en fragmentanalyse reacties opruimen van samples aanenten en isoleren van DNA samples maken en runnen van agarose gelen uitvoeren van kwaliteitcontroles schoonmaak en klein onderhoud van apparatuur We zijn op zoek naar Enthousiaste flexibele gedreven en resultaatgerichte kandidaten die liefst in de buurt van Leiden woonachtig zijn en full time 40 uur per week willen werken Je hebt interesse en ervaring in uitvoer van moleculaire technieken Je kan onder druk van deadlines nauwkeurig en resultaatgericht blijven werken Je bent in staat om zowel zelfstandig als in teamverband te werken en hebt goede communicatieve vaardigheden Goede kennis van de Nederlandse en Engelse taal is een vereiste Ervaring met het werken volgens kwaliteitssystemen ISO17025 en GMP en microbiologische ervaring is een pré Opleidingseis voor deze functie is een voltooide opleiding op MLO niveau met minimaal

    Original URL path: http://www.baseclear.com/career-jobs/Moleculair-Biologisch-Analist-%28m/v%29_30_12.html (2016-02-12)
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  • Baseclear
    to submit their genome sequence often need help from an internally available bioinformatician or receive help from partners such as BaseClear to get this job done To help the scientific community in facilitating genome submissions we have published an article in collaboration with the bioinformatics group of the Wageningen University The aim is to save valuable time and money when submitting your genome sequences but also the article provides some feedback for organizations that are responsible for genome and functional databases to put more focus on data standardization and facilitate clearer acceptance criteria This blog is a short overview of our findings for the complete article see http bib oxfordjournals org content early 2015 12 10 bib bbv104 short rss 1 Preparing genome sequences for a GenBank submission is not straightforward Building an annotated genome involves genome assembly structural annotation and functional annotation and requires proper validation after each step There are many tools and pipelines available for this task and although FASTA GFF and GenBank are considered standard formats methods produce a great variety in output both in content and file format The NCBI aims to convert output into standardized database formats For this they offer conversion tools to make sure that the same rules apply to all genomes entered Despite their efforts scientist experience many different issues arising from genome submissions The recommendations below are targeted at researchers that want to submit their data In the complete article more details can be found The article also provides suggestions for the developers of assembly annotation and submission tools which are not discussed in this blog The NCBI aims to convert output into standardized database formats Despite their efforts scientist experience many different issues arising from genome submissions Recommendations for NCBI compliant genome assembly submissions It is strongly recommended to remove foreign DNA before the annotation to submit the clean assembly and only on acceptance by GenBank annotate the genome It is important to make full use of GenBank s error reports otherwise some issues preventing submission will remain invisible Recommendations for NCBI compliant structural genome annotations It is recommended for researchers to specify or check the minimum intron lengths during annotation and to have a close look at the gene properties including exon and intron lengths before submission It is the responsibility of the user to explicitly annotate fiveprime and three prime partial genes in the feature table format a five column tab delimited table of feature locations and qualifiers In addition tbl2asn generates a warning if a partial gene does not start on a consensus splice site but partial genes are often annotated differently At present the NCBI also allows submission of annotated scaffolds rather than contigs A problem that may arise during the annotation of scaffolds is that some prediction tools allow start and end sites within the gaps This is not accepted by GenBank these features will have to be removed before submission which can be time consuming if done manually The problem could be avoided

    Original URL path: http://www.baseclear.com/blog/How-to-overcome-complex-NCBI-compliant-genome-submissions-and-the-importance-of-data-standardization_40_8.html (2016-02-12)
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  • Nucleid acid extraction is an essential part of your sequencing project
    2012 Although mechanical lysis by bead beating to homogenize samples offers a better penetration of the lysis buffer through the complete sample it may result in a higher degree of DNA shearing The latter may be detrimental to whole genome sequencing endeavours that rely on input of high molecular weight DNA Salonen et al 2010 Henderson et al 2013 However methods employing a bead beating step do appear to generate largest DNA yields with higher microbial Bacteria Archaea and fungi numbers and diversity estimates Salonen et al 2010 Henderson et al 2013 Quigley et al 2012 Shearing of the DNA can be minimized by removing the aqueous phase after each round of beat beating that are employed to lyse remaining cells Salonen et al 2010 Yu and Morrison 2004 Though chemical and enzymatic lysis methods are gentler they do not fully access all microbial populations in the sample owing to the irregular biostructure described above Our own evaluation of different bead beat apparatuses revealed that the apparatus itself as well as homogenization time indeed has a profound influence on the overall DNA yield Figure 1 However extracted DNA amounts did not show an gradual increase with more and longer homogenization steps which is most likely due to the fragment specifics used for extraction Analysis of the DNA by agarose electrophoresis showed that even at high speeds and prolonged homogenization most DNA was high molecular weight Figure 2 Figure 1 Extracted DNA yield with differing homogenization time and apparatus employed for DNA extraction from a single fecal sample A and agarose gel with 5 l extracted DNA after 30 minutes of electrophoresis B Apparatus 1 was used at its maximum speed of 30 vibrations per second while apparatus 2 was used at one of its intermediate speeds of 5500 rpm The method of extraction can have a strong bias on the quantification of total bacteria and abundance estimations of specific taxonomic groups These observations affirm that the extraction methodology is a strong determinant for the outcome of microbial profiling and other DNA RNA based techniques including metagenomics and transcriptomics Furthermore we tested commercially available DNA extraction kits on several different fecal samples and measured DNA yield using a fluorometric essay This revealed that there were profound differences in terms of DNA yield Figure 2 indicating that the choice of DNA extraction method influences how much starting material is required and practical progress of the sequencing project in terms of speed Figure 2 Comparison of two commercially available kits for DNA extraction of DNA from feces collected from human adult A and human baby B Samples were stored at room temperature RT frozen at 80 C and in a DNA stabilisation buffer SB prior to DNA extraction It is far from trivial to assess which extraction method yields the nucleic acid fraction that represents the true microbial composition most accurately Henderson et al 2013 Although previous studies have shown that the extraction methodology itself can have a profound impact on the outcome

    Original URL path: http://www.baseclear.com/blog/nucleic-acid-extraction-is-an-essential-part-of-your-sequencing-project_40_7.html (2016-02-12)
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  • DNA sequencing platforms, a short overview
    There have been mentions of Oxford Nanopore sequencing output of 1 Gb to 2 Gb per minION and read lengths of 20 kb to 120 kb What makes this platform really promising is the expected low price and the compact size Because it is so small hand held sequencing devices are becoming a reality ILLUMINA The current marked leader in the area of NGS is Illumina They have around 70 of the market in hands They are dominating the market with the MiSeq NextSeq HiSeq and HiSeqX series The principle of Illumina sequencing is based on the incorporation of fluorescently tagged nucleotides into the clonally amplified DNA templates Each of the four bases has a unique emission The Illumina platform characterizes itself through short reading lengths 50 300 nt and low to high output 0 5 M 2000 M reads With the Illumina platform you can also make use of so called paired end reads Here clonally amplified DNA templates are read in two directions Through this a longer reading length can be reached of up to 2x300 nt The Illumina platform can be considered as the best price per nt and can be used for all forms of DNA and RNA sequencing projects ranging from amplicon sequencing and genome sequencing to RNA sequencing THERMO FISHER SCIENTIFIC The runner up with around 15 market share is Thermo Fisher Scientific TFS At the moment TFS has three devices on the market namely the Ion Proton Ion PGM and Ion S5 The platform of TFS is based on ion semiconductor sequencing Here DNA sequencing is based on the detection of hydrogen ions that are released during the polymerization of DNA The out put ranges from 100 Mb to 32 Gb Read lengths range from 100 to 400 nt The applications for this platform ranges from amplicon sequencing to RNA sequencing in other words diverse ROCHE The number three in the market with around 8 market share is Roche Their 454 pyrosequencing platform with the GS Junior GS FLX was once the golden standard for amplicon sequencing However Roche announced that they will stop the support for this platform in 2016 Therefore most users are switching to the Illumina MiSeq The output ranges from 35 Mb to 700 Mb with read lengths of 700 nt up to 1kb PACIFIC BIOSCIENCES Pacific Biosciences PacBio has the number four platform on the market They have a market share of 5 At the moment they have one device on the market and one that is coming shortly In chronological order PacBio RSII and the Sequel system The PacBio platform differs from the aforementioned NGS platforms In contrast to the other NGS platforms the PacBio platform does not work with a spatially separated clonally amplified DNA templates but with single DNA molecules The full name of this technique is Single molecule real time sequencing SMRT Here a single DNA polymerase is fixed on the bottom of a zero mode waveguide ZMW which is part of a SMRT

    Original URL path: http://www.baseclear.com/blog/DNA-RNA-sequencing-platforms-a-short-overview_40_6.html (2016-02-12)
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  • Oxford Nanopore is here to stay: ready for the challenges?
    technical issues arbitration may be be Standardization of the gDNA preparation would be beneficial we are all going back to the basics and using old fashioned techniques to make sure the high molecular weight DNA is of really high molecular weight If we fast forward to 2015 the picture is very different three and a half years after the first presentation at AGBT the MinION early access program has yielded an increasing number of exciting peer reviewed publications and datasets the chemistry and nanopores are being constantly improved as well as the base calling algorithms With read lengths reaching easily the 60 70 kb for 2D reads it is the quality and integrity of the input DNA that has become the limiting factor Adalberto Costessi interviewed Hans Jansen to discuss his view on these developments Adalberto Costessi Hans you seem very enthusiastic about your experience with MinIons so far How is the collaboration with ONT going Hans Jansen I am very excited about our collaboration and Oxford Nanopore has a quite different way of working and communicating compared to the big sequencing providers They are very open and they provide a lot of information about their plans through forum and blog posts and during the MinION early access program they met all the milestones they had announced AC You have recently participated to ONT s London calling user meeting What s in the pipeline for the short term HJ The current MinION MkI has 512 nanopores of which about 300 are functional and the DNA moves at about 30 bases second through the pores The new MinION version MkII will be released early next year including 3000 nanopores 6x increase and ONT is also about to release for beta testing a new fast mode sequencing option in which the DNA should go through the pores at 500 bases second 16x faster These updates will tremendously increase the data output AC What about the error rate HJ The current error rate per base is about 8 which is a bit lower than PacBio however the errors are not completely random and rather show some bias Moreover homopolymer regions are very hard to call because if the bases are all the same you cannot distinguish well how many exactly went through the pore There are however tricks to address this issue ONT announced that they expect to reach a 1 error rate before the end of 2015 which would be a great achievement AC What applications have you worked on so far at ZF screens HJ At ZF screens we have a peculiar interest in the assembly of large vertebrate genomes The data output of the first generation MinION is not sufficient to support such studies which require large datasets Therefore we rather focused on small microbial genomes so far mostly bacteria and some yeasts However this year the larger platform PromethION will become available for testing which will make it possible to run 48 MinION s MkII flowcells in parallel This

    Original URL path: http://www.baseclear.com/blog/Oxford-Nanopore-is-here-to-stay-ready-for-the-challenges-_40_5.html (2016-02-12)
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  • Bacterial genome analysis using Oxford Nanopore sequencing technology
    molecule to be sequenced through multiple passes to build a more accurate consensus read The technology has not yet matched second generation platforms in terms of sequence quality but has proven useful in various applications including contig scaffolding In the past years we have put much effort in creating workflows which involves a hybrid analysis approach where both Illumina short reads and PacBio long reads are combined to create closed genomes of extremely high quality Not only lab protocols are optimized also a full data analysis pipeline called SSPACE LongRead Boetzer and Pirovano 2014 has been developed whereas the Illumina technology typically generates genome assemblies comprising 20 500 contigs mainly due to the presence of repetitive elements which are larger than the short read length the addition of PacBio long reads generally leads to a fully closed bacterial genome one contig per chromosome and possible plasmids Will we be able to easily close bacterial genomes in a high throughput manner when read lengths go beyond 100Kbp though with an error rate of approximately 10 But change is coming The latest long read sequencing technologies in particular that of Oxford Nanopore Technologies have the potential to further ease the process and importantly breakdown the analysis costs So called USB stick DNA sequencing is promised to have an enormous strong impact on genomic research as the library preparation and sequencing steps will gradually become only a fraction of the costs of current long read sequencing technologies As a matter of fact Oxford Nanopore Technologies started in 2014 with an early access program of their first robust sequencer The MinION Access Program MAP Likewise the PacBio system it delivers long read real time sequencing of individual molecules It is the first commercial nanopore based rather than synthesis based sequencer The MinION is quite small and portable having the size of a USB stick The current throughput is still limited but quickly increasing to several Giga bases per run And this isn t yet all in 2015 the PromethION will be offered in an early access program which is a small benchtop system for high throughput real time biological analyses and allowing larger sample numbers This will give a further boost to the technology and make it suited for sequencing 96 wells plate in no time Meanwhile different solutions are being developed for easy and on site library preparations can it be a matter of time before this becomes routine work And when will these solutions become available for a large audience and not only through an advance access program And will we be able to easily close bacterial genomes in a high throughput manner when read lengths go beyond 100Kbp though with an error rate of approximately 10 It seems that the revolution has started and no wonder the participants of the recently held London Calling meeting where different partners of the MinION advanced access program presented their findings returned home with a huge smile on their face and a personalized MinION But

    Original URL path: http://www.baseclear.com/blog/bacterial-genome-analysis-using-oxford-nanopore-sequencing-technology_40_4.html (2016-02-12)
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  • Potential of the DNA barcoding of Life project
    Although efforts to complete the barcoding of all species are being done in many countries The Netherlands were putting in a large bit as part of the FES funding of this project Both Naturalis as CBS Centraalbureau voor Schimmelcultures received a large sum of money to get a better picture of the biodiversity in the Netherlands As BaseClear we are very proud to say that we had part in this great endeavour by supplying our sequencing services to the project It is estimated that 1 9 million species have been described so far where this project has generated over 3 7 million different barcodes already and shows that that there most likely more than 8 million species out there Why would you like to embark on such a project Off course there are many scientific reasons why this project is very interesting Not only will it give a more and better insight in the diversity in nature Personally I find the most striking fact that we still do not know and have described most species living on this planet It is estimated that 1 9 million species have been described so far where this project has generated over 3 7 million different barcodes already and shows that that there most likely more than 8 million species out there Also the way evolution has brought all these species on earth is something that gains more insight through this project It helps to understand how the tree of life is constructed and which species were developed during evolution As a life science entrepreneur I am also intrigued by the potential of possible applications that follow from this project Several presentations during this day focused on applications that were developed during the project or will be developed with the results of the project Off course an easier and cost effective way to identify species is useful in monitoring the environment If you can do this in bulk or in high throughput by using DNA methods you have a simple tool available to see which valuable species are living in certain areas DNA technology has as an extra advantage that it can be used on a diversity of sample types so you need not always have access to a living individual of the species itself but can do monitoring on a very small part other body materials or even for instance faeces of the species Applications that were presented or come to mind are the identification of imported endangered species the identification of processed species in food products think of the scandal around horse meat and the use of DNA barcoding in forensic criminal cases dog or cat hairs found on crime scenes microbial diversity in soil on footprints that can be traced back typing of insects found on bodies One of the projects in which we actively participate is a project with KWR and Naturalis and several other partners where we look at the potential to use DNA and more detailed e DNA

    Original URL path: http://www.baseclear.com/blog/the-potential-of-the-DNA-barcoding-of-life-project_40_3.html (2016-02-12)
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