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→Build Binary Reference Genome and Word Index
karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa
karma --colorSpace --createReference --createIndex --reference NCBI36CS.fa
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When building the index files one can set the word length for indexing. We recommend N = 15 (the default value) for the human genome on a machine with at least 20 Gb of RAM. Shorter index words will decrease the memory footprint at the cost of increased run time. However, the word length must not be longer than half the length of the color space reads you intend to map, minus 1. (See [[#Choose_an_appropriate_size_for_word_index|Choose an appropriate size for word index]] for more discussion.) Specify ``--wordSize N`` in order to use ''N'' as the word size.<br>
When building the index files, one can set the word length for indexing. We recommend N = 15 (the default value) for the human genome on a machine with at least 20 Gb of RAM. Shorter index words will decrease the memory footprint at the cost of increased run time. However, the word length must not exceed half the length of the color space reads you intend to map, minus 1. (See [[#Choose_an_appropriate_size_for_word_index|Choose an appropriate size for word index]] for more discussion.) Specify ``--wordSize N`` in order to use ''N'' as the word size.<br>
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