A mapping of the new program names to the old program names is contained in the distribution in a file called clc_name_changes.txt.
For Linux and Mac users, a script has been included as an example of how you could update the Assembly Cell program names in existing scripts you have. The script is called change_clc_names.sh. If you plan to use the script without changes, please read through it first, to make sure that it will do what you need.
Below is a listing of the old names followed by the new names for the CLC Assembly Cell programs:
assembly_info --> clc_mapping_info assembly_table --> clc_mapping_table castosam --> clc_cas_to_sam change_assembly_files --> clc_change_cas_paths clc_assembly_viewer --> clc_mapping_viewer clc_novo_assemble --> clc_assembler clc_ref_assemble_long --> clc_mapper_legacy clc_ref_assemble --> clc_mapper filter_matches --> clc_filter_matches find_variations --> clc_find_variations host_info --> clc_host_info join_assemblies --> clc_join_mappings join_pairs --> clc_overlap_reads quality_trim --> clc_quality_trim remove_duplicates --> clc_remove_duplicates samtocas --> clc_sam_to_cas sequence_info --> clc_sequence_info simulate_reads --> clc_simulate_reads sort_pairs --> clc_sort_pairs split_sequences --> clc_split_reads sub_assembly --> clc_submapping tofasta --> clc_convert_sequences unassembled_reads --> clc_unmapped_reads unpaired_reads --> clc_unpaired_reads