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<br> We show a complete example demonstrating the whole procedure from building the word index to mapping color space reads in [[#A_Complete_Example|A Complete Example]].
<br> We show a complete example demonstrating the whole procedure from building the word index to mapping color space reads in [[#A_Complete_Example|A Complete Example]].
= Build Binary Reference Genome and Word Index<br> =
= Build Binary Reference Genome and Word Index =
First, build a binary version of the genome reference sequence as nucleotides (option: --createReference). Suppose that NCBI36.fa is a FASTA file which contains nucleotide sequences for all chromosomes.<br>
First, build a binary version of the genome reference sequence as nucleotides (option: --createReference). Suppose that NCBI36.fa is a FASTA file which contains nucleotide sequences for all chromosomes.
The command to invoke is:<br>
The command to invoke is:
karma --createReference --reference NCBI36.fa
karma --createReference --reference NCBI36.fa
