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= Build Binary Reference Genome and Word Index<br> =

= Build Binary Reference Genome and Word Index<br> =

&nbsp; First, we need to build binary reference genome (option: --createReference)<br> &nbsp; &lt;ref&gt;To let KARMA map nucleotide space reads, you need to use ``--createIndex''to create the word index file.&lt;/ref&gt;''<br>

&nbsp; First, we need to build binary reference genome (option: --createReference)<br> &nbsp;  

<ref>To let KARMA map nucleotide space reads, you need to use ``--createIndex''to create the word index file.</ref><br>

&nbsp; in nucleotide space. Assume NCBI36.fa is a FASTA file contains sequences of all chromosomes.<br> &nbsp; The command to invoke is:<br>

&nbsp; in nucleotide space. Assume NCBI36.fa is a FASTA file contains sequences of all chromosomes.<br> &nbsp; The command to invoke is:<br>

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!!1111111111111111111111111111111111</pre>  

!!1111111111111111111111111111111111

</pre>  

== Minimum read length requirement ==

== Minimum read length requirement ==