Fosmid libraries provide long range linking information that can vastly improve the size of an assembly’s scaffolds. Whilst these optional libraries are not required for small genomes, we do recommend them if you are trying to assemble anything large. However, building libraries with insert sizes of ~40 kb can be very difficult.
To this end, the Broad Institute has developed a new method called “Fosill” for creating such libraries. Our manuscript “Paired-end sequencing of Fosmid libraries by Illumina” was recently posted as an accepted preprint in Genome Research. Please direct any questions on the method to the paper’s corresponding author.