Category

Mapping


Usage

bwa index [-p prefix] [-a algoType] <in.db.fasta>


Manual

OPTIONS:

  • -p  STR  Prefix of the output database [same as db filename]
  • -a  STR  Algorithm for constructing BWT index. Available options are:
    • is  IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. The current codes for IS algorithm are reimplemented by Yuta Mori.
    • bwtsw  Algorithm implemented in BWT-SW. This method works with the whole human genome.


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