REFRESH Bioinformatics Group


MuGI—What is it?

Multiple Genome Index is a compressed index of collections of genomes of the same species. It allows to ask for both exact and approximate queries. The input data must be given as a reference sequence and Variant Call Format (VCF) file describing the differences between individual genomes and reference genome.

The architecture of MuGI

MuGI is composed of several programs that were used in our experiments on the genomes from the 1000 Genomes project. A description of the tool can be found in our paper (see below).

How good is MuGI?

The collection of 1092 diploid human genomes (6.7TB of raw sequences) can be stored in 6.5–32GB of RAM. The software is configurable and different tradeoffs can be chosen depending on what is more important: fast queries or so small size that fits even a PC with 8GB of RAM. For the moderate settings the index occupies 11.4GB of RAM and for patterns of length 120–170 answers: exact queries in 43μs, 2-mismatch queries in 151μs, 5-mismatch queries in 4461μs. All matches up to given threshold in all individuals are reported. (Test machine: 3.4GHz i7 4770 CPU.)

For more details please consult our paper.

Terms of use of MuGI

MuGI is in general a free compression program available in source code releas. More details can be found out on download page.


+ Danek, A., Deorowicz, S., Grabowski, Sz., Indexes of Large Genome Collections on a PC, PLOS ONE, 2014; 9(10):e109384, Abstract.

The availability of thousands of individual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. Its unique feature is the small index size, which is customisable. It fits in a standard computer with 16–32 GB, or even 8 GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries (of average length 150 bp) are handled in average time of 39 μs and with up to 3 mismatches in 373 μs on the test PC with the index size of 13.4 GB. For a smaller index, occupying 7.4 GB in memory, the respective times grow to 76 μs and 917 μs. Software is available at under a free license. Data S1 is available at PLOS One online.