Building Index for BWA

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

The dialog looks as follows:

The parameters are as follows:

• Reference sequence — the DNA sequence to which short reads will be aligned. This parameter is required.

• Index file name — the file in which to save the index. This parameter is required.

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

  • is — designed for short reads up to ~200bp with a low error rate (<3%). It performs gapped global alignment with respect to reads, supports paired-end reads, and is one of the fastest short-read alignment algorithms to date while also visiting suboptimal hits.

  • bwtsw — 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 default value “autodetect” means that the index (one of three) is chosen automatically depending on the length of the sequence.