CLC mapping

At ths point, the most current version of the CLC command-line utils is located here:

/usr/local/packages/clc-ngs-cell/

with the mapper for 454 / Sanger reads being clc_ref_assemble_long.

As usual, you need to copy the license.properties file from that folder to your working directory to perform any sort of analysis.

Here are some of the pitfalls:

- making a soft link to the mapping executable will throw a missing license error. forget the soft link, you need to use the fully qualified path of the executable.

- mapping to a Genbank file didn't work. However mapping to a FASTA file completed with blazing quickness.

Once the mapping has producea CAS output, you need to process it to get it in table format:

/usr/local/packages/clc-ngs-cell/assembly_table -n -s input.cas > output.table