- 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.
- 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.
The read mapper "clc_mapper" has been replaced by a new memory efficient mapper.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.
- 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.
- 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.
- Fixed problem with read mapping on computers with Japanese Windows.
For a complete list of older release, visit the CLC Assembly release archive.