- Added a new parameter --normaltypelimit (-S) to 'clc_mapper' for specifying the read length to be applied when deciding when to switch to long read mapping. The default value is 500 (bp), which guarantees the same default behavior as the previous version (Assembly Cell 5.0.5).
- Added a new parameter --mappermemory (-M) to 'clc_mapper' that allows the amount of memory (MB) to be used during mapping to be restricted. This parameter needs to be set when --normaltypelimit (-S) is used, since the memory usage increases with the squared read length, which can potentially cause the system to run out of memory. The -M parameter overrides the --cpus parameter to ensure a lower memory usage.
- Fixed a very rare bug in 'clc_mapper', where an alignment with a leading unaligned end could result in a wrong score
- Fixed a bug where 'clc_correct_pacbio_reads' would segfault if not given an output file
- Fixed a bug where the argument --interleave was not accepted by the tool 'clc_quality_trim'
- 32 bit versions of the QIAGEN CLC Assembly Cell are no longer distributed.
The tools 'clc_mapper_legacy' and 'clc_remove_duplicates' will be retired starting from Assembly Cell 6.0 onward. They will remain present on older release lines. If you are concerned about the proposed changes, please contact our Support team firstname.lastname@example.org