To build BWA index select the Tools ‣ NGS data analysis ‣ Build index for reads mapping item in the main menu. The Build Index dialog appears. Set the Map short reads method parameter to BWA.

The dialog looks as follows:

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There are the following parameters:

Reference sequence — DNA sequence to which short reads would be aligned to. This parameter is required.

Index file name — file to save index to. This parameter is required.

Index algorithm (-a) — Algorithm for constructing BWA index. Available options are:

It implements three different algorithms

• • is — designed for short reads up to ~200bp with low error rate (<3%). It does gapped global alignment w.r.t. reads, supports paired-end reads, and is one of the fastest short read alignment algorithms to date while also visiting suboptimal hits.
  • bwtsw — is designed for long reads with more errors. It performs heuristic Smith-Waterman-like alignment to find high-scoring local hits. Algorithm implemented in BWA-SW. On low-error short queries, BWA-SW. is slower and less accurate than the is algorithm, but on long reads, it is better.
  • div — does not work for long genomes.

The value "autodetect" by default means that the index (one of three) is chosen automatically depending on the length of the sequence.