In order to run CLC Bio programs from the command line, you need to have a license.properties file in your current working directory. But not any license.properties file, the one associated to the specific version of software you are using. For example, if you are using a command that is on the path, you need to track down which license.properties file it is associated with.
Mapping reads - (greater than 50 bp in length):
For mapping reads back to a reference which have 90% identity over 90% of the length of the query
/usr/local/packages/clc-ngs-cell-2.0.5-linux_64/clc_ref_assemble_long -o < output.cas > -q < query.fasta > -d < database.fasta > -l 0.9 -s 0.9
The output of this mapping, or reference-based assembly, is a .cas file. Getting a table of hits, a la nucmer, you need to process the .cas file with another CLC tool: assembly_table
Processing .cas files:
/usr/local/packages/clc-ngs-cell-2.0.5-linux_64/assembly_table -n -s < output.cas > > < table.tsv >
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