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* Binary reference genome in nucleotide space (see [[#Input file requirement|Input file requirement]]})
* Binary reference genome in nucleotide space (see [[#Input file requirement|Input file requirement]]})
* 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 \ref{sec:4.1} 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 \ref{sec:4.2})
* Specify color space parameter when starting KARMA (see \ref{sec:3})<br>
* Specify color space parameter when starting KARMA (see \ref{sec:3})<br>
==Input file requirement==
==Input file requirement==
KARMA require input files in valid color space FASTQ format.<br> We require the length of reads(including leading primer) should equal to the length of its quality string.<br> <br> A valid example of color space FASTQ file:<br>
KARMA require input files in valid color space FASTQ format.<br> We require the length of reads(including leading primer) should equal to the length of its quality string.<br> <br> A valid example of color space FASTQ file:<br>
!!1111111111111111111111111111111111
!!1111111111111111111111111111111111
== {{anchor|sec4.2}}Minimum read length requirement ==
==Minimum read length requirement==
Keep in mind that the requirement of minimum color space read length for KARMA is<br> twice the size of word plus two (including leading primer) \footnote{For nucleotide space,<br> the minimum length requirement is twice the word size.}.<br> For example, KARMA use word size of 15 by default, so it will try to map color space<br> reads that are longer than 32 base pairs.<br>
Keep in mind that the requirement of minimum color space read length for KARMA is<br> twice the size of word plus two (including leading primer) \footnote{For nucleotide space,<br> the minimum length requirement is twice the word size.}.<br> For example, KARMA use word size of 15 by default, so it will try to map color space<br> reads that are longer than 32 base pairs.<br>
== {{anchor|sec4.3}} Auxiliary tools ==
==Auxiliary tools==
ABI SOLiD platform generated FASTA file (e.g. XXX.csfasta) and quality file (e.g. XXX\_QV.qual) separately. We wrote a script, ''solid2csfastq.py'', to convert it to color space FASTQ file(e.g. XXX.csfastq). We believe a single color space FASTQ file will simplify post processing.<br>
ABI SOLiD platform generated FASTA file (e.g. XXX.csfasta) and quality file (e.g. XXX\_QV.qual) separately. We wrote a script, ''solid2csfastq.py'', to convert it to color space FASTQ file(e.g. XXX.csfastq). We believe a single color space FASTQ file will simplify post processing.<br>
== {{anchor|sec4.4}} Choose an appropriate size for word index ==
==Choose an appropriate size for word index==
Size for word index is sensitive to mapping performance. A small size of word index will increase the number of calculation cycles for a single read and duplications of a single word. On the other side, a big size will require much larger memory. Please also keep in mind that appropriate size is related to your hardware architecture. For practically purpose, we found size of 15 is optimal.
Size for word index is sensitive to mapping performance. A small size of word index will increase the number of calculation cycles for a single read and duplications of a single word. On the other side, a big size will require much larger memory. Please also keep in mind that appropriate size is related to your hardware architecture. For practically purpose, we found size of 15 is optimal.
