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* Binary reference genome and word index in color space (see \ref{sec:2})
* Binary reference genome and word index in color space (see \ref{sec:2})
* Color space reads in valid color space FASTQ format (see [[#Input file requirement|Input file requirement]] for file specification)
* Color space reads in valid color space FASTQ format (see [[#Input file requirement|Input file requirement]] for file specification)
* Color space reads are longer than minimum length requirement. (see \ref{sec:4.2})
* Color space reads are longer than minimum length requirement. (see [[#Minimum read length requirement|Minimum read length requirement]])
* Specify color space parameter when starting KARMA (see \ref{sec:3})<br>
* Specify color space parameter when starting KARMA (see \ref{sec:3})<br>
karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa
karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa
An important parameter is the size of words for indexing.<br> We recommand 15 (default value) for human reference genome.<br> Specifiy ``--wordSize N`` if you like to use $N$ as word size.<br> Typically you will observe performance change (see \ref{sec:4.4} for more discussion).<br> <br> <br> Note, multiple chromosomes are supported.<br> In current version, KARMA can take one FASTA file which contains sequences of all chromosomes.<br>
An important parameter is the size of words for indexing.<br> We recommand 15 (default value) for human reference genome.<br> Specifiy ``--wordSize N`` if you like to use $N$ as word size.<br> Typically you will observe performance change (see [[#Choose an appropriate size for word index|Choose an appropriate size for word index]] for more discussion).<br> <br> <br> Note, multiple chromosomes are supported.<br> In current version, KARMA can take one FASTA file which contains sequences of all chromosomes.<br>
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