Home Software Services About Contact usearch manual
Read mapping

Read mapping is a straightforward application of the UBLAST algorithm, though the default options may not give an optimal balance between sensitivity and speed. Use the ublast command with a UDB database. Assuming a typical scenario where the reads have high identity with a reference genome, I recommend building the database with -wordlength 14. Further speed improvements may be obtained by reducing -dbaccel, I suggest testing values in the range 70 to 90. My testing shows that these parameters give speeds that are typically around 50x faster than bowtie with better sensitivity.