Microbial communities are more and more analyzed by direct
sequencing of DNA from environmental samples. The aim is to
study the microbial composition at different conditions and the
identification of novel organisms. The bottleneck is the
assembly of the metagenome reads. Why are these assemblies so
challenging? One important reason is the highly heterogeneous
character of the microbial environmental sample. Furthermore the
abundance of the member species differs remarkably. While some
species are highly abundant, others – often the unknown and
therefore very interesting ones – are present at a very low
level. In order to receive contigs from the low abundant species
very deep sequencing is needed and these species often can only
be assembled in a highly fragmented manner. Another challenge
for metagenomic assemblies are populations of closely related
species. As their genomes are highly similar the assembly
software generates hybrid contigs from those closely related
species. Despite or probably due to thes