Bug fixes

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

Improvements

• Improvement of the long reads mapper to find more matches

New features

• New program to remove duplicate reads.
• New tool to do quality trimming of sequencing data.
• New tool to convert CAS files to SAM/BAM format and vice versa.
• New option in the reference assembly and assembly table programs to track and retrieve multiple hit positions for a read.
• It is now possible to restrict cpu usage of all the assembly programs
• The progress output for the assembly programs can be switched off using the –no-progress option
• In the assembly viewer, you can now press K and enter the number of the contig you want to jump to

Bug fixes

• Various minor bug fixes in the assembly programs

Bug fixes

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

Updates

• 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.

Updates

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

Updates

• Fixed color space bug

New features

• Option to manually specify word size
• Option for verbose output (e.g. word size used)

• 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

Updates

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

CLC NGS Cell 2.0.3

Release date: April 28, 2009

Updates

• Various bug-fixes

CLC NGS Cell 2.0.2

Release date: April 21, 2009

Updates

• Various bug-fixes

CLC NGS Cell 2.0.1

Release date: February 26, 2009

Updates

• 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