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Tool name, like bwa, HISAT2 etc.

Short usage hints, like

bwa index [-p prefix] [-a algoType]

Like

Index database sequences in the FASTA format.

Parameter list of this tool, like

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.

Link to the tool's documentation or DOI id of the paper.

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