CLC Genomics Workbench free download, CLC Genomics Workbench download on software download

Allows you to analyze and visualize Next Generation Sequencing data. CLC Genomics Workbench our new solution for analyzing and visualizing Next Generation Sequencing data. CLC Genomics Workbench incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.CLC Genomics Workbench is very fast and allows you to do reference assembly of genomes of any size - the only limit is the amount of RAM on the machine running the software. CLC Genomics Workbench is also able to support SNP detection, de novo assembly and a large number of downstream analysis. Here are some key features of "CLC Genomics Workbench": · De novo assembly of Sanger, 454, Illumina Genome Analyzer, Helicos, and SOLiD data. · Reference assembly of Sanger, 454, Illumina Genome Analyzer, Helicos, and SOLiD sequencing data. · Reference assembly of mixed datasets (e.g. 454 and Illumina Genome Analyser). · Reference assembly of genomes of any size. · Assembly of standard read data and support for assembly of paired end reads / mate pair reads of any sequencing technology. · Advanced graphical tools for detection of large scale mutations and rearrangements. · Single reads - coverage and conflicts. · Paired-ends reads - graphical overview. · Paired-ends reads - insertions and deletions. · Paired-ends reads - duplications and inversions. · Support for multiplex sequencing by file name. · Support for multiplex sequencing by sample-specific tag. · Masking of reference assembly based on annotations like e.g. exons. · Integration with CLC bio’s High Performance Computing solutions, making assemblies very fast. · Interactive and zoom-able viewing of genome assemblies, including sequencing reads, quality data, and reference sequences. Full integration of the viewers with the downstream analyses. · Quality reporting and statistics on raw data. · This wizard is used to handle parallel tagged sequence data. The use of tagged samples can dramatically increase sequencing throughput of next generation sequencers . Analysis of this sample of mixed data is done by the Genomics Workbench. · Matthias Meyer, Udo Stenzel & Michael Hofreiter, "Parallel tagged sequencing on the 454 platform", Nature Protocols 3, - 267 - 278 (2008) · This wizard is used to handle parallel tagged sequence data. · Filtering and trimming of reads. · Advanced SNP detection. · SNP reporting. · Support for integration with CLC Bioinformatics Database. Requirements: · 256 MB RAM required. · 2 GB RAM recommended. · 1024 x 768 display recommended. · 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards). · Assembly and analysis of genomes up to 10 mega-bases: 2 GB RAM required; 4 GB RAM recommended. · Assembly and analysis of larger genomes: 2 GB RAM required; 8 GB RAM recommended. · 64 bit computer and operating system recommended for more than 2 GB RAM. Limitations: · 30 days trial period. What's New in This Release: · Global alignment for long reads when running reference assembly algorithm · Gapped color-space alignment when running reference assembly · Significantly improved speed of all operations with large data sets RNA-Seq analysis: · Performance optimization: A run of 44 mio reads against the mouse genome now takes 32 minutes on an eight-core computer with 32GB RAM. This used to be more than two hours. With the previous version, a lot of small temporary files were created and deleted, and this took a long time and impacted the comupter's general responsiveness. In comparison, only a small fraction of temporary files are created with the new version. · New option to specify minimum required exon-overlap of reads spanning an exon-exon junction. Read more... · New RNA-Seq report which gives statistical overview of the assembly process. Read more... · Result table now reports number of exon-exon- and intron-exon junction spanning reads. · Result table now reports chromosome location of genes. Read more... · Visualization of reads that span exon-exon junctions. Read more... · Reads mapping equally well to intron-exon and exon-exon boundaries are now identified as unique exon-exon spanning reads. · RPKM is better defined in the user manual. Read more... · Default setting for multi-hits is now 10 as in the Mortazavi paper Read more... · Very short reads are now assembled allowing more mismatches. Expression analysis: · Volcano plots: you can now choose the values to plot on the x-axis. Choose between "Difference" and "Fold change". Read more... · Table view of bar plots shows the same intervals as are shown in the bar plot. · Generic importer for expression array data in tabular format. Read more... · Generic importer for expression experiment annotation data in tabular format. Read more... · Gene Ontology (GO) files can now be used to annotate an expression experiment. Read more... · Tag profiling: You are no longer allowed to annotate tag samples, only experiments · Side panel of experiment table has been re-organized to provide better overview. Read more... Import high-throughput sequencing data: · Import tool moved from Toolbox to File menu and tool bar. Read more.. · Import and export of the SAM alignment format. Read more... · Import of alignment data in tab-delimited format, including the ELAND alignment format. Read more... · Import of Illumina QSEQ file format. Read more... · Linker in 454 data is also found for non-perfect matches Read more... Enhanced visualization of contigs: · Un-aligned nucleotides on the inside of paired-end reads are now shown · Paired-end reads have a single line connecting the pair rather than gaps · Drag handles to move the aligned/unaligned border are only shown when you can see the bases of the reads. This means that you need to have zoomed in to 100% or more and chosen Compactness levels "Not compact" or "Low". Otherwise the handles for dragging are not available (this is done in order to make the visual overview more simple). Read more.... · It is possible to display pairs that overlap · The unassembled reads from an assembly now preserves their paired-end status (this also means that you can get two lists - one with pairs and one with the remainder of the broken pairs · SNP detection output table now reports if multiple non-synonymous SNPs exist in same codon · SNP detection dialog: Quality filtering is no longer disabled when quality scores are missing. Due to performance issues it is not possible to check if quality scores are present. The SNP detection will just omit the quality score filtering if quality scores are not present. · SNP detection: possible to detect variants with frequency less than 1 percent. · Contig report now includes information about coverage for both covered regions and whole reference. Read more... · Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends · The trim functionality now includes the option to trim away a predefined number of nucleotides from either end of a read. Read more... · Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones. Read more... · Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments. Read more... · In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu. Read more... · Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments. Read more... Deployment: · You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more... · Support for removing tools accessing the internet (NCBI BLAST, update notifications etc). Read more... General import and export: · Support for import of complex regions from GFF files · Export tables and reports in Excel format. · Import section of user manual re-structured to provide better overview Read more.... Expression data importers are now described in technical details in a separate section Read more.... · You can now export multiple sequence lists in fasta format · Forced import of zip files is now supported (it will force import the contents of the zip file) · The standard import now accepts gzip and tar files as well as zip · If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files · Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: "product", "locus_tag", "protein_id" and "transcript_id" · When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted. · When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales) · GFF plug-in has been updated to accept complex annotations Miscellaneous: · Advanced retyping of annotations using the annotation table. Read more... · Improved reporting of situations when a full disk prevents saving of data · Downloading sequences using drag and drop from the search table no longer creates a "Downloading..." node in the folder. The download process can be monitored in the Processes tab. · Primer design now supports PCR fragments longer than 5000 bp. · Extract Sequences moved from File manu to Toolbox-> General Sequence Analysis. Read more... · Better progress feedback on various dialogs Bug-fixes: · Problem with order of genes when setting up RNA-Seq experiments. If the order of input sequences was not the same for all samples, the experiment would be wrong. · Fixed wrong orientation of SOLiD mate-pair data · Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X). · Fixed problem displaying the "Copying..." label when copying data and then updating the folder · Misleading label when assembling reads shorter than 15 bp. Now it says that these reads will be ignored in assembly

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