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Appendix A
Updating program names from earlier
versions
The names of the programs of CLC Assembly Cell have changed since version 3.2.2 and earlier.
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
assembly_table
castosam
change_assembly_files
clc_novo_assemble
clc_ref_assemble_long
clc_ref_assemble
filter_matches
join_assemblies
join_pairs
quality_trim
remove_duplicates
samtocas
sequence_info
simulate_reads
sort_pairs
split_sequences
sub_assembly
tofasta
unassembled_reads
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clc_mapping_info
clc_mapping_table
clc_cas_to_sam
clc_change_cas_paths
clc_assembler
clc_mapper_legacy
clc_mapper
clc_filter_matches
clc_join_mappings
clc_overlap_reads
clc_quality_trim
clc_remove_duplicates
clc_sam_to_cas
clc_sequence_info
clc_simulate_reads
clc_sort_pairs
clc_split_reads
clc_submapping
clc_convert_sequences
clc_unmapped_reads
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