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

&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>

&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>

<br>

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  Second, we need to build binary reference genome (option: --createReference) and word index (option: --createIndex)

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

  in color space. The same FASTA file is needed. However, to avoid naming conflicts, we suggest using word "CS"  

  appending to the base file name for clarity. The command to invoke is:

   ln -s NCBI36.fa NCBI36CS.fa

   ln -s NCBI36.fa NCBI36CS.fa

== Minimum read length requirement ==

== Minimum read length requirement ==

&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>

&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>

== Auxiliary tools ==

== Auxiliary tools ==