Building Index for BWA-SW

To build a BWA-SW 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-SW.

The dialog looks as follows:

The following parameters are available:

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

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

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

Algorithm	Description
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. The algorithm is implemented in BWA-SW. On low-error short queries, BWA-SW is slower and less accurate than the is algorithm, but for long reads, it is better.
div	Does not work for long genomes.

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