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Latest improvements for QIAGEN CLC Assembly Cell

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QIAGEN CLC Assembly Cell 3.2.2

Release date: 2011-04-04

Bug fixes

  • Fixed problem with read mapping on computers with Japanese Windows.

QIAGEN CLC Assembly Cell 3.2.1

Release date: 2011-04-04


  • Improvement of the long reads mapper to find more matches

QIAGEN CLC Assembly Cell 3.2

Release date: 2010-11-05

New features

Bug fixes

  • Various minor bug fixes in the assembly programs

QIAGEN CLC Assembly Cell 3.1.1

Release date: 2010-04-19

Bug fixes

  • Fixed error mapping large data sets on Windows 64-bit systems.

QIAGEN CLC Assembly Cell 3.1

Release date: 2010-06-15


  • The sequence_info program supports multiple files
  • The tofasta program has been improved:
    • Option to discard read names (-d)
    • Option to produce a fastq format rather than fasta by supplying a quality score file
    • Option to create a random subset of a read file (using the -f option)
  • The split_sequences program has been improved to make sure no linker sequence is left in the reads. In addition, the following has been improved:
    • Option to choose between Titanium and FLX linkers (-d)
    • Option to include several linker sequences
  • The find_variations program has new options to specify the treatment of gaps in the assembly.

QIAGEN CLC Assembly Cell 3.0.3

Release date: 2010-04-06


  • Fixed error when de novo assembling more than 1 billion reads

QIAGEN CLC Assembly Cell 3.0.2

Release date: 2010-03-22


  • Fixed color space bug

QIAGEN CLC Assembly Cell 3.0.1

Release date: 2010-03-16

New features

QIAGEN CLC Assembly Cell 3.0

Release date: 2010-03-12

  • New de novo assembler
  • Name change from CLC NGS Cell to QIAGEN CLC Assembly Cell
  • De novo assembly of large genomes
  • Inclusion of option to use paired reads for guidance only
  • Fixed bug with large data sets on Windows

CLC NGS Cell 2.1

December 04, 2009

New features

  • Support for gapped color space assembly
  • Option to do global alignment of long reads
  • Option to do gapped global alignment, also for short reads
  • Option to do semi-global alignment
  • More flexible license locations
  • Various bug fixes

CLC NGS Cell 2.0.5

Release date: July 13, 2009


  • Now dots (unknown colors) are allowed in csfasta files
  • Various bug-fixes

CLC NGS Cell 2.0.3

Release date: April 28, 2009


  • Various bug-fixes

CLC NGS Cell 2.0.2

Release date: April 21, 2009


  • Various bug-fixes

CLC NGS Cell 2.0.1

Release date: February 26, 2009


  • Support for license server
  • Find_variations program has more options. Read more
  • Various bug-fixes

CLC NGS Cell 2.0

Release date: January 14, 2009

New features

  • De novo assembly
  • Assembly in native color space format
  • Long reads assembler significantly faster (up to 15x faster)
  • Option for global alignment using ungapped short reads
  • Support for csfasta format
  • Support for Scarf format
  • Assembly viewer: New options to search for a sequence motif
  • Temporary files are placed in the directory specified by TMP (Windows) and TMPDIR (Mac and Linux) variables

Bug fixes

  • Find_variations program optimized to avoid out-of-memory errors
  • Sub_assembly og non_assembled_reads can be output in fastq format (by file name)

CLC NGS Cell 1.0

Release date: September 18, 2008

Main features

  • Reference assembly of Sanger, 454, Solexa, Helicos, and SOLiD sequencing data
  • Assembly of genomes of any size (only limited by RAM available)
  • Assembly of standard read data and support for assembly of paired end reads / mate pair reads of any sequencing technology
  • Integration with QIAGEN CLC Genomics Workbench for user friendly downstream analyses using a graphical user interface
  • Quality reporting and statistics on raw data
  • 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.
  • Find variations (simple SNP detection)
  • Support for input file formats Fasta, Sff, and GenBank
  • A number of output options, including tables with assembly info
  • A “graphical” (ASCII art :-)) assembly viewer to get quick overview
  • Runs on Windows, Mac OS X, and Linux