Read mapping

Read mapping is a fundamental step in most analyses of high-throughput sequencing data. It involves aligning sequencing reads to a reference genome or sequence to determine their most likely origin.

A typical analysis begins with mapping reads to a reference using Map Reads to Reference or Map Long Reads to Reference, followed by Local Realignment to correct misalignments around indels, and when relevant, Remove Duplicate Mapped Reads to reduce bias due to PCR amplification or other enrichment. These steps ensure an accurate read mapping, providing a reliable foundation for any further analysis.

Several other tools, such as Map Reads to Contigs, RNA-Seq Analysis, or Map Bisulfite Reads to Reference, can also perform read mapping. This chapter focuses on the core tools.


Subsections