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  • Microbial profiling - BaseClear
    identification and diversity studies BaseClear offers complete solutions to extract DNA from your samples and the means to determine the composition of bacteria and also for Archaea and fungi in a broad range of sample including water faeces and bioreactor specimens The technical approach for this kind of studies is usually based on PCR amplification followed by sequencing of housekeeping or functional genes for instance 16S 18S 23S or ITS The generated data is then compared to microbial sequencing databases Data analysis is performed by our in house developed tool the BaseClear metaGenome Browser BmGB Advantages of microbial diversity analysis also referred to as microbial profiling 16S profiling or 16S metagenomics studies based on Next Generation sequencing compared to classical methods include Identify thousands of microorganisms in one analysis Identification of non cultivable microorganisms Determine the relative abundance of microorganisms Extremely fast for screening of complex ecosystems Better understanding and control of the microbial flora Microbial diversity analysis using Next Gen sequencing can be applied in a wide variety of studies For instance in food processing probiotics water safety testing microbiome analysis biofilms fermentation soil research e g Rhizobia and environmental samples WHY CHOOSE OUR MICROBIAL DIVERSITY ANALYSIS SERVICE BaseClear is specialized in microbial diversity studies for environmental e g food water and soil and microbiota samples We offer complete solutions based on 16S for bacteria and or ITS for fungi amplicon analysis for taxonomic classification and determine relative frequencies Our managers are happy to discuss the ideal workflow that best fits your needs and budget Our main drive is to make sure that your research questions are answered Our advantages include BaseClear has a strong focus on microbial genomics Many years of experience with microbial profiling projects with samples coming from a variety of different source e g soil

    Original URL path: http://www.baseclear.com/genomics/next-gen-sequencing/microbial-profiling (2016-02-12)
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  • Bioinformatics services - BaseClear
    of bioinformatics solutions primarily in the area of Next Generation Sequencing NGS data analysis Our aim is to offer state of the art analysis which guarantee our customers to receive high quality results and provide clear answers to their research questions Our excellent bioinformatics team can assist you with answering a wide range of genomics questions from assembly to comparative genomics to metagenomics and expression analysis as well as custom analyses Results are delivered in a secure fast and comprehensive manner and are the ideal starting point for your downstream interpretation Our customers can rely on a top level Next Gen lab infrastructure including the latest sequencing technologies offered by Illumina and Pacific Biosciences Our Next Gen team which take care of the full process from isolation to library preparation and sequencing of high quality reads make sure you are always up to date about the status of your project And of course you can always ask our specialists to provide consultancy support to define the optimal project setup The data generated is carefully processed and analysed by our bioinformatics team thus offering you a complete analysis solution from wet lab to data interpretation In this manner BaseClear profiles itself as a fast reliable and complete solution provider Since 2013 we also assist our customers with unique online portals which allow them to interactively visualize and interpret their data Be it comparative genomics or metagenomics our online viewing and analysis platforms are extremely handy tools to mine your genomes of interest and extract the most important information in only a few clicks But there is more For instance our BaseTools section the place where we share our scientific expertise with the community Here you can read more about out high impact publications such as the SSPACE assembly and the King

    Original URL path: http://www.baseclear.com/genomics/bioinformatics (2016-02-12)
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  • Genome assembly and annotation - BaseClear
    assembled into a finished genome followed by in depth annotation The annotated genomes are imported into our secure online portal which allows the customer to interactively mine and compare genomes GENOME ASSEMBLY Our bioinformatics department has developed state of the art assembly pipelines which follow a reference based or De Novo approach and in some cases a combination of both The ultimate goal is to provide our customers with a high quality finished genome sequence To accomplish this task we offer different sequencing approaches among which Illumina HiSeq Illumina MiSeq and PacBio RS II with SMRT technology platforms The resulting reads are optimally merged into finished genomes using the best available tools in the market for draft assembly error correction scaffolding and gap closure We also offer different options for quality assessment and control Two examples of assembly quality control figures in the left panel the coverage distribution of all contigs is displayed in the right panel a BLAST search is shown where the compact clusters indicate that the library contains a single organism E coli Delivered output Assembled contig and scaffold sequences in FastA format Alignment file BAM and sorted alignment index file BAI in case of reference guided assembly AGP Accession Golden Path file describing the linkage between contigs in the scaffolds This format is required for WGS submissions to the NCBI De Novo assembly report containing a summary of the assembly results and quality measures ANNOTATION Often a stretch of nucleotide sequence is not the ideal output format of a sequencing experiment In such scenario BaseClear can offer high quality annotations In brief we first define the most likely gene structure model for bacteria with Prodigal software and for eukaryotes with Augustus software Subsequently we assign functional annotations to genes inclusive of EC GO and CAZy numbers

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/genome-assembly-and-annotation (2016-02-12)
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  • Comparative genomics - BaseClear
    genome At BaseClear use a combination of powerful analysis to address these questions At this moment we offer standard whole genome alignments and variant detection services VARIANT DETECTION BaseClear has years of experience with variant detection With this service you will receive the reference alignments in BAM format the sorted alignment index files in BAI format the consensus sequences in FastA format and a table containing detailed information on found variants SNPs single base substitutions SUBs multiple base substitutions and insertions and deletions A summary of the found variants and alignment statistics is presented in a variant detection report Example of a read alignment ADVANTAGES OF OUR VARIANT DETECTION SERVICE Quality filtering and trimming of reads in order to start the analysis with high quality sequences Reference alignment is performed using the state of the art aligner of the CLCbio Genomics Workbench Variant calling is also performed with the quality based algorithm of the CLCbio Genomics Workbench Stringent parameters are used among which Quality score evaluation of the alignment position and surrounding bases Usage of forward and reverse mappings Limited allowance of mismatches Coverage and multi redundant hit removal The final output is provided in comprehensive Excel tables which can be customized for multiple samples to easily compare different samples Example of a SNP table WHOLE GENOME ALIGNMENTS Our Whole genome alignment WGA provides more insight into the different genomic architecture between genomes In brief sequence alignments are constructed between a number of genomes and the output consists of a comprehensive overview of structural variations that lie at the basis of differential functional behaviour This analysis can be performed by customers themselves using our online BaseClear Genome Browser BGB the Compare module features a unique tool to compare multiple genomes through alignment and interactively analyse genetic variations between sequenced genomes

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/comparative-genomics (2016-02-12)
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  • RNA-seq analysis - BaseClear
    which follow a reference based or De Novo approach and in some cases a combination of both The ultimate goal is to provide our customers with the best possible answers to their transcriptome analysis research questions To accomplish this task we generally use the Illumina HiSeq sequencing platform If no annotated reference genome is available we are able to generate high quality De Novo transcriptome assemblies with Trinity Grabherr et al 2011 and subsequently annotate transcripts using our in house annotation pipeline Based on an annotated reference genome and mRNA sequencing reads gene expression levels are calculated using the CLC Genomics Workbench The approach taken for sample normalization is based on Mortazavi et al 2008 Graphical overview of an RNA Seq alignment which is the basis for expression analysis BaseClear customers receive in addition to expression tables also the corresponding BAM and BAI alignment files QUALITY CONTROL AND STATISTICAL INTERPRETATION Our standard service also includes a number of quality control steps based on the overall distribution of expression analysis in the samples These results in publication ready figures such as a comparative box plot a principle component analysis PCA scatter plot and a hierarchical clustering figure to inspect inter and intra group variability Also we include a significance assessment of differentially expressed genes following a well defined statistical analysis In this manner differentially expressed genes are reliably determined through the assignment of P values The exact approach is defined by the type of experiment used e g comparison between two or multiple groups or the presence absence of biological replicates Two examples of RNA Seq expression analysis quality control figures in the left panel a box plot shows overall distribution of the expression values in the samples Biological repeats have the share the same color in the right panel a

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/RNA-seq-analysis (2016-02-12)
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  • Microbial profiling analysis - BaseClear
    and our main drive is to make sure that your research questions are answered A schematic overview of a 16S amplicon based approach Illumina MiSeq reads are merged into overlapping pseudo reads and subsequently aligned against a 16S database Taxonomic classification is performed using an in house protocol Extended advice on the project setup and in depth downstream analysis are provided in collaboration with our partner NIZO Food Research 16S BASED AMPLICON ANALYSIS Our bioinformatics department has developed two state of the art microbial profiling analysis pipelines The 16S based amplicon analysis protocol generally involves the Illumina MiSeq sequencing platform which is capable of producing paired end reads of length 300 nt Alternatively also the Illumina HiSeq and PacBio SMRT platforms can be used to generate shorter and longer reads respectively Depending on your research question and available budget BaseClear can offer the best possible strategy that guarantees an optimal output In most cases Illumina MiSeq paired end reads are generated which are merged into overlapping pseudo reads using our bioinformatics analysis pipeline In this manner a relatively long stretch of the 16S rRNA gene can be covered e g the V3 V5 region with single reads Subsequently each read is aligned against a 16S rRNA gene database for taxonomic classification The standard output includes a comprehensive table containing all taxonomies found and their counts but also a number of publication ready figures which allow an easy graphical interpretation of the findings e g a cladogram piechart and barchart The results can also be easily viewed and compared in an interactive manner using our unique online BaseClear metaGenome Browser BmGB Click here to read more about our interactive online metaGenome Browser Our 16S amplicon based analysis protocol includes the generation of easy to interpret tables and figures For example the

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/microbial-profiling-analysis (2016-02-12)
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  • Bioinformatics - Interactive online platforms
    ONLINE PLATFORMS The bioinformatics specialists at BaseClear have developed interactive online platforms which are specifically designed to provide customers with interactive tools to easily interpret their Next Generation sequencing data These online tools are the ideal starting point for viral bacterial and fungal genome analysis be it a single genome a complete strain collection or a metagenomic community They constitute a safe repository for all your samples and can be viewed without any software installation At present there are three different portals for each a comprehensive manual is available BaseClear Genome Browser BGB https annotation baseclear com A portal to mine and compare whole genomes Read more BaseClear metaGenome Browser mBGB https metagenomics baseclear com Multilevel taxonomic analysis across 16S amplicons Read more Virus diagnostics 2 0 https virusdiagnostics baseclear com On the fly analysis of viral communities in plants and animals Read more Server security and data integrity is guaranteed through through SSH server client connections and additional security measures Licenses are generally freely offered in combination with our sequencing and bioinformatics packages and valid for one year For additional questions or a free trial please contact us at info baseclear com ADVANTAGES OF OUR ONLINE BIOINFORMATICS PORTALS Safe repository of your genomic data stored at an independent service provider Free license in combination with a sequencing bioinformatics project Easy and fast screening of multiple samples and strain collections up to 10 000 samples Specifically designed for analysis of viruses and bacterial and fungal communities Advanced search functions and local BLAST Unique genome comparison module to detect similarities differences between strains Multiple options for export of results i e figures tables etc No installation of software needed Online portals are supported by Firefox Internet Explorer version 9 and higher and Chrome No additional fee for multiple users easy way

    Original URL path: http://www.baseclear.com/genomics/bioinformatics/online-platforms (2016-02-12)
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  • BaseTools software - BaseClear
    the area of Next Generation Sequencing NGS data analysis For this we mainly make a choice out of the most advanced software packages available on the market However especially in such a dynamic field as NGS we frequently develop our own software solutions to fill in the gaps that are not covered by existing tools Some of our analysis setups are published in collaboration with other groups in some cases we decide to share stand alone tools with the scientific community At present our bioinformatics team has published a number of high impact papers which underscores the scientific excellence of our team We see our tools and pipelines as important features that are part of our complete solutions packages In this manner we can guarantees our customers to receive outstanding results that fully answer their research questions Current BaseTools software SSPACE standard SSPACE longread GapFiller MOST IMPORTANT PUBLICATIONS SSPACE LongRead scaffolding bacterial draft genomes using long read sequence information Boetzer M Pirovano W BMC Bioinformatics 2014 Jun 20 15 211 doi 10 1186 1471 2105 15 211 The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system Vonk FJ Casewell NR Henkel CV Heimberg AM Jansen HJ McCleary RJ Kerkkamp HM Vos RA Guerreiro I Calvete JJ Wüster W Woods AE Logan JM Harrison RA Castoe TA de Koning AP Pollock DD Yandell M Calderon D Renjifo C Currier RB Salgado D Pla D Sanz L Hyder AS Ribeiro JM Arntzen JW van den Thillart GE Boetzer M Pirovano W Dirks RP Spaink HP Duboule D McGlinn E Kini RM Richardson MK Proc Natl Acad Sci U S A 2013 Dec 17 110 51 20651 6 doi 10 1073 pnas 1314702110 SNP genotyping for detecting the rare allele phenomenon in hybrid zones Lammers Y Kremer

    Original URL path: http://www.baseclear.com/bioinformatics-tools (2016-02-12)
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