Building Index for BWA-MEM

To build a BWA-MEM 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-MEM.

The dialog looks as follows:

The parameters are as follows:

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

Index file name — File where the index will be saved. This parameter is required.

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

It implements three different algorithms:

• is — Designed for short reads up to ~200bp with a low error rate (<3%). It does 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 value “autodetect” by default means that the index (one of three) is chosen automatically depending on the length of the sequence.