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→Build Binary Reference Genome and Word Index
(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'' 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). The same nucleotide FASTA file is used. However, to avoid naming conflicts among the resulting binary files, we suggest appending "CS" to the base file name for clarity. The command to invoke is:<br>
Second, one also needs to build color space versions of both the genome reference sequence (option: --createReference) and the word index files (option: --createIndex). The same nucleotide FASTA file is used. However, to avoid naming conflicts among the resulting binary files, we suggest appending "CS" to the base file name for clarity. The command to invoke is:<br>
ln -s NCBI36.fa NCBI36CS.fa
ln -s NCBI36.fa NCBI36CS.fa
