Sample & Assay Technologies
Click here to learn more

CLC Assembly Cell – Latest Improvements

CLC Assembly Cell 4.4

Release date: February 24, 2015


    • The clc_find_variations tool has now been moved to the deprecated folder and will not be part of future releases.
    • A new tool named clc_extract_consensus has been introduced which can extract consensus sequences from a cas file.
    • The default read mapper now support affine gap cost.
    • Maximal length of reference sequences has been increased from 1Gbp to 2Gbp.



    • Introduced an option in clc_overlap_reads for automatic removal of adapter sequences in overlapping reads.
    • Introduced an option in clc_filter_matches for removing both reads of a read pair if just one of the reads fails to pass the filter criteria.
    • When performing a read mapping with affine gap cost, alternating gaps in a read and reference is now prevented by default.
    • Progress measuring in read mapper and de novo assembler made smoother.


Bug fixes

    • clc_cas_to_sam now supports all integer types for the NH tag which fixes the erroneous error message "Wrong type for CS tag" in most cases.
    • Fixed rare crash in clc_mapping_table and clc_remove_duplicates.
    • Fixed a bug which could cause the read mapper to report sub-optimal alignments when using affine gap cost in rare cases.
    • Fixed a crash for the read mapper which could occur when the input read file contained several reads shorter than 15bp.
    • Fixed a crash that occurred on older CPUs when using very long reference sequences.

CLC Assembly Cell 4.3

Release date: August 28, 2014

New Features

  • The read mapper "clc_mapper" has been replaced by a new memory efficient mapper. The quality and speed of the read mapping matches the previous mapper.

  • A beta version of the memory efficient read mapper that supports affine gap cost is available under the name "clc_mapper_beta".

  • The clc_mapper has an updated interface with improved feedback to the user and colors.

  • The read mapper now accepts paired reads with a distance of up to 100kbp.

  • For machines with many cores the performance of the k-mer counting step in the de novo assembler has been improved.

  • Fastq quality score offset is now auto detected in the tools "clc_quality_trim" and clc_overlap_reads".

  • Added support for gzipped reference sequences.

  • Improved the speed of the legacy read mapper on gzipped input files.

  • castosam now reports quality scores that are compatible with samtools.

Bug fixes

  • The progress indicator for the de novo assembler now behaves correctly in the interval 90-92%.
  • Fixed a collision of temporary file names that could cause the de novo assembler and read mapper to crash.
  • The default gap cost in clc_overlap_reads is now set to 3 as stated in the documentation. It used to be 2.


  • The SCARF read format is now deprecated and will be removed in future versions of the CLC Assembly Cell.
  • The clc_find_variantions tool is now deprecated. Functionality for computing consensus sequences will be made available in a separate tool while the variant detection functionality will be removed in future versions of the CLC Assembly Cell.

  • Support for 32 bit versions of the Apple OS X operating system is deprecated and a distribution of the CLC Assembly Cell will not be available for this platform in the future.

  • The clc_mapping_viewer tool has been removed.

CLC Assembly Cell 4.2.1

Release date: January 23, 2014

Bug fixes

  • Fixed a bug in the de novo assembler that caused circular contigs containing scaffolds to be output with a negative scaffold size in AGP format.
  • Fixed a bug in the read mapper that could result in a crash for reads longer than 20Kbp.
  • Fixed a bug that caused the mapper to report wrong paired read distances when mapping to circular genomes.


  • From version 4.3 of the Assembly Cell the program clc_mapping_viewer will be removed.

CLC Assembly Cell 3.2.2

Release date: April 11, 2011


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

Old Releases

For a complete list of older release, visit the CLC Assembly release archive.