How do I quickly align sequencing reads against a reference sequence.

Align to reference is a perfect tool for mapping small sequencing projects against a reference sequence. It’s perfect for accurately and quickly:

Confirming the sequence of a cloned fragment.
Sequencing across the ends of a cloned fragment to confirm the junction sequence.
Screening clones from a site-specific mutagenesis experiment to identify successful mutations.
Screening related clones for single nucleotide polymorphisms
Screening sequenced reads for CRISPR INDEL modifications.

See the Align to reference help topic for more details.