Importing and Demultiplexing Sequence Data Quick Reference

The following is a “pocket guide” to determining the appropriate methods for importing and demultiplexing FASTA/FASTQ sequences (primarily from marker-gene sequencing experiments). Many samples are often “multiplexed” (pooled and sequenced together) on a single sequencing run. So the first step to analyzing these data is to demultiplex the data. Often, demultiplexing is performed automatically by sequencing centers/services and users. How can you tell if you have demultiplexed data? If you have one sequence file (or pair of files) per sample. The following steps are meant as a guide to determine appropriate steps and tutorials for importing (and demultiplexing) sequence data.

If you find errors in this guide, or want to provide steps for importing or demultiplexing other formats, get in touch!