Since then, BGI has grown rapidly and is partner in a number of international consortiums, including partnerships with the Wellcome Trust Sanger Institute, NIH and NHGRI on the 1,000 Genomes Project. CLC Genomics Workbench takes full advantage of "paired end" data and supports a number of features and work-tasks, such as reference assembly of genomes, de novo assembly of genomes, SNP detection using advanced models, multiplexing, and high-throughput trimming.īeijing Genomics Institute is one of the leading global Genomics Institutes in the world, established in July 1999. CLC Genomics Workbench will help the scientists at BGI with their daily research, including prestigious projects like the Giant Panda Genome Project and the 1000 Genomes Project," said Michael Heltzen, director of partner sales, CLC bio.ĬLC Genomics Workbench is the first comprehensive analysis package which can analyze and visualize data from all the major NGS platforms, such as Solexa by Illumina, SOLiD by Applied Biosystems, 454 by Roche Applied Science, and HeliScope by Helicos. RNA Seq Analysis tool in the Biomedical Genomics Analysis plugin of the CLC Genomics Workbench was used to extract all annotated transcripts using both Homo. Furthermore, we are honored that the famous bioinformatics researchers from BGI have chosen our Workbench as a working platform for both our and their own algorithms, side by side. "We are most thrilled to have agreed on a global site license with one of the best bioinformatics and sequencing facilities in the world, only four weeks after our solution for analyzing and visualizing Next Generation Sequencing data was released. mapped to Syrian hamster genome (BCMMaur2.0 (GCF017639785.1) Differential expression determined between Ad14 and Ad14p1 infected samples with CLC Genomics Assembly: BCMMaur2.0 (GCF017639785. In no time, CLC Genomics Workbench has proved amazingly popular with our internal researchers, due to the fast, user-friendly and versatile platform it provides." fastq files were imported into CLC Genomics Workbench and reads were trimmed. We can support and expand our workflows by giving our scientists easy access via the Workbench to our own in-house developed algorithms. In an organization of our size - with seventeen Illumina GA analyzers, as well as two AB/SOLiD and three Roche/454 Next Generation Sequencing machines, all of them running at full capacity - efficient workflows are of critical importance. Head of Bioinformatics Division at BGI, Ruiqiang Li states, "We have chosen CLC Genomics Workbench as our platform for analyzing Next Generation Sequencing data after testing several commercial solutions, because it's simply in a league of its own when it comes to flexibility and the way the Next Generation Sequencing tools can be used together with our own algorithms. The site license covers all researchers at all BGI sites, both inside and outside of China. To obtain the homology based genes MAKER aligned reference ESTs and proteins using Blastx and exonerate against the macadamia scaffolds.Beijing Genomics Institute (BGI) has signed a global site license agreement for CLC bio's Next Generation Sequencing solution, CLC Genomics Workbench. In parallel, known repetitive sequences were identified using the RepeatMasker program with the latest release of RepBase curated repeat libraries.Īnnotation of gene models was conducted using MAKER (version 2.31.8) which combines the power of protein and Expressed Sequence Tag (EST) based homology with ab initio gene predictions to produce polished gene annotations. Putative repetitive sequences were identified using the RepeatModeler program with default parameters. Genome assembly was performed in the following two steps: preliminary contig assembly using PE reads in CLC, followed by assembly of sequence contigs and filtered high quality MP reads using the scaffolding program SSPACE to obtain a final set of scaffolds. MP reads were also trimmed to remove low quality bases and adapter sequences. Paired-end sequence reads were trimmed to remove low quality bases and adapter sequences and de novo assembled using CLC Genomics Workbench (CLC) version 6.5 (CLC Bio, Aarhus, Denmark). Paired-end libraries (PE) with average insert sizes of 480 and 700 bp and an 8 kb MP library were prepared using Illumina TruSeq DNA Sample Preparation kit v2 following manufacturer’s instructions. Total genomic DNA was extracted using a DNeasy Plant Maxi kit for all DNA sequencing with the exception of mate pair (MP) library sequencing where DNA was extracted using a CTAB-based method developed for next-generation sequencing. Prior to DNA and RNA extraction, leaf tissue was frozen in liquid nitrogen and ground using a tissue lyser. Fresh plant tissue was collected from a Macadamia integrifolia and stored at -80 ☌.
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