SUMMARY: MGI sequencing is reported to be an inexpensive solution to obtain genomics information. There is a growing need for software and tools to analyse MGI's outputs efficiently. mgikit is a tool collection to demultiplex MGI fastq data, reformat it effectively and produce visual quality reports. mgikit overcomes several limitations of the standard MGI demultiplexer. It is highly customizable to suit different kinds of datasets and is designed to achieve high performance and optimal memory utilization. AVAILABILITY AND IMPLEMENTATION: The tool and its documentation are available at: https://sagc-bioinformatics.github.io/mgikit/.