Changes

= 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;  

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

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

== Minimum read length requirement ==

== Minimum read length requirement ==

&nbsp; Keep in mind that the requirement of minimum color space read length for KARMA is<br> &nbsp; twice the size of word plus two (including leading primer) <br>

&nbsp; Keep in mind that the requirement of minimum color space read length for KARMA is twice the size of word plus two (including leading primer).<br>&nbsp; (For nucleotide space, the minimum length requirement is twice the word size.)<br> &nbsp; For example, KARMA use word size of 15 by default, so it will try to map color space reads that are longer than 32 base pairs.<br>

(For nucleotide space,<br> &nbsp; the minimum length requirement is twice the word size.).<br> &nbsp; For example, KARMA use word size of 15 by default, so it will try to map color space<br> &nbsp; reads that are longer than 32 base pairs.<br>

== Auxiliary tools ==

== Auxiliary tools ==

= A Complete Example =

= A Complete Example =

&nbsp; A wrap-up message for quick start mapping color space reads.<br>

&nbsp; A wrap-up message for quick start mapping color space reads.<br>