BWA-MEM
BWA is a fast, lightweight tool designed to align relatively short reads to a reference sequence. Click this link to open the BWA homepage. BWA-MEM is generally recommended for high-quality queries, as it is faster and more accurate. BWA-MEM also performs better than BWA-backtrack for 70-100bp Illumina reads.
Open the Tools ‣ Align to reference submenu from the main menu.
Select the Align short reads item to align short reads to a DNA sequence using BWA-MEM. Alternatively, select the Build index item to build an index for a DNA sequence, which can be used to optimize the alignment of short reads.