Read alignment, commonly referred to as read mapping, is the process of matching sequence reads to a reference sequence.

For example, you can map reads to a reference genome to identify where on a reference genome that read most likely originated, and through alignment determine the optimal matching against the reference sequence.

Read mapping is a fundamental primary analysis step in many workflows such as variant detection, transcript isoform annotation, or even differential gene expression.

Alignment typically requires input as FASTQ file and generates the sequence alignment/map format call SAM format or the binary equivalent, BAM.

Many of our analysis workflows already include alignment steps as described on the EPI2ME page. Read mapping can also be performed during basecalling through our software MinKNOW and Dorado.

For third-party tools, please see their GitHub pages for installation and usage. To address any issues with these and other third-party tools, please post to the Issues tab on the individual GitHub repositories as we cannot offer support for third-party software.