Changes

   karma --createReference --reference NCBI36.fa

   karma --createReference --reference NCBI36.fa

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(To let KARMA map nucleotide space reads, one would use instead ''--createIndex'' to create both a binary sequence and the word index files.)<br>

(To let KARMA map nucleotide space reads, one would use instead ''--createIndex''&nbsp; to create both a binary sequence and the word index files.)<br>

Second, we also need to build color space versions of both the genome reference sequence (option: --createReference) and the word index files (option: --createIndex).&nbsp;  The same nucleotide FASTA file is needed.&nbsp;  However, to avoid naming conflicts among the resulting binary files, we suggest appending "CS" to the base file name for clarity.&nbsp;  The command to invoke is:<br>

Second, we also need to build color space versions of both the genome reference sequence (option: --createReference) and the word index files (option: --createIndex).&nbsp;  The same nucleotide FASTA file is used.&nbsp;  However, to avoid naming conflicts among the resulting binary files, we suggest appending "CS" to the base file name for clarity.&nbsp;  The command to invoke is:<br>

   ln -s NCBI36.fa NCBI36CS.fa

   ln -s NCBI36.fa NCBI36CS.fa