Features in CLC Assembly Cell

Read mapping

  • Read mapping of Illumina, Pacific Biosciences, Ion Torrent, SOLiD, and 454 sequencing data
  • Native support for Color Space
  • Support for both short read and long read assembly
  • Support for both gapped and ungapped alignments when doing short read mapping
  • Support for mapping of paired end reads

De novo assembly

  • De novo assembly of Illumina, Pacific Biosciences, Ion Torrent and 454 sequencing data
  • Support for both short read and long read assembly
  • Support for de novo assembly of paired end data
  • Building scaffolds from paired-end data

Other analyses

  • Fast analysis of raw data, including reporting
  • Option of joining data from different sources into the same analysis (including data generated by different kinds of sequencing technologies)
  • Extraction of data from part(s) of an assembly. Examples are extraction of contig and reads from an area of interest, or extraction (exclusion) of data from a specific sequencing lane that is suspected not to be of acceptable quality.
  • Removal of duplicate reads
  • Quality trimming
  • Find variations (simple SNP detection)
  • Support for input file formats Fasta, Sff, GenBank, csfasta, and scarf
  • A number of output options, including tables with assembly info
  • Full integration with CLC Genomics Workbench and Biomedical Genomics Workbench – output data from CLC Assembly Cell can be imported and further analyzed in CLC Genomics Workbench and Biomedical Genomics Workbench

More information about CLC Assembly Cell

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