The NCBI RefSeq database was used to obtain a number of known or homologous genes from the assembled transcript sequences.” By contrast, “ The CLC GW assembly output contained a list of assembled transcripts and unassembled sequence reads.” Want to know if you’re seeing something new? Open the finished assembly in SeqMan Ultra to view known and novel transcripts separately in two highly customizable and sortable reports.Īccording to the study authors, SeqMan NGen “produced both annotated and novel transcripts lists. Lasergene Genomics supports many options for downstream analysisĪfter de novo transcriptome assembly, other applications in the Lasergene Genomics package allow different types of downstream analysis. The comparison study found that SeqMan NGen “…clearly defines excluded reads in its project report…” By contrast, SeqMan NGen reports which reads were excluded. Software that lacks the ability to report excluded reads may be oversampling the reads, reducing the precision of the transcriptome assembly. SeqMan NGen reports whether contaminant sequences were present The total count of transcript fragments that aligned and matched RefSeq sequences provides the sequencing coverage. Many data sets assembled with SeqMan NGen produce a large number of long transcripts that are likely full-length transcripts. How does SeqMan NGen do it? SeqMan NGen automatically attempts to group contigs from the same gene, and then name and annotate them based on the best match to a collection of annotated reference sequences (the “Transcript Annotation Database”) extracted from data on NCBI’s RefSeq website. The study authors noted that “ … the Lasergene SMN Trace Evidence consensus-calling algorithm generated longer contigs on average…Meanwhile, CLC GW had assembled over nine times the amount of contigs…” Using its proprietary assembly algorithm, however, SeqMan NGen creates fewer and longer contigs than CLC Genomics Workbench. Performing meaningful downstream analysis on this many unannotated contigs is nearly impossible. With other applications, de novo assembly of RNA-Seq data can potentially result in thousands of unlabeled contigs representing the expressed transcripts. We support all the major next generation sequencing platforms, such as SOLiD, Ion Torrent, Complete Genomics, 454, Illumina Genome Analyzer and of course also Sanger, and we are working closely together with all the instrument vendors to ensure full integration in the ongoing development.ĬLC Genomics Workbench supports read mapping as well as de novo assembly of hybrid data.SeqMan NGen assembly output contains fewer and longer contigs It includes a number of features within the fields of genomics, transcriptomics and epigenomics, and additionally it includes all the tools of CLC Main Workbench. We have overcome the challenge to analyze high-throughput sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our next generation sequencing solution, CLC Genomics Workbench – a cross-platform desktop application with a graphical user-interface.ĬLC Genomics Workbench, for analyzing and visualizing next generation sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.ĬLC Genomics Workbench is available for Windows, Mac OS X, and Linux platforms. Dominating the high-throughput sequencing data analysis challenge
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