deletions | additions       diff --git a/Library Preparation and Sequencing .md b/Library Preparation and Sequencing .md  index e5e2187..afc97cc 100644  --- a/Library Preparation and Sequencing .md  +++ b/Library Preparation and Sequencing .md 
...
##Multiplexing  The capacity of an Ilumina MiSeq with PE300bp reads is around 15 Gb which would result in a coverage of 4300X for a typical bacterium with a 3.5Mb genome. On the HiSeq with PE125bp reads, this would be over 14,000X coverage. Currently, the recommended coverage for a bacterial genome assembly is 30-100X depending on the choice of assembler. Therefore, sequencing a single bacterial genome on a full MiSeq or HiSeq run is a significant waste of money and reagents. Furthermore, current genome assembly algorithms do not perform well given an excess of data, and require down-sampling (i.e., throwing away data) to acheive the recommended coverage for assembly. We typically multiplex 10-20 genomes on a PE300bp MiSeq run and many more on a HiSeq run. If using a kit for library prep, multiplexing is quite straightforward since there are a number of barcoded adaptors that come with the kit. Demultiplexing can be performed by the sequencing facility.  ##Collaborations ##Collaborate  Given the overcapacity of Illumina sequencing for bacterial genomes, doing sequencing  a single genome presents a problem (unless willing to pay the ~$2000 total cost and throw away most of the data). Sequencing facilities will typically not "pool" samples from multiple groups because they don't want to oversee the pooling or deal with the associated billing accounting  hassles. In this case, However,  collaborating with other groups would can  be the most logical a great  option. Many labs sequence genomes or metageomes on a regular basis, basis;  adding in one additional sample isn't technically  very difficult. difficult, but it will entail oversight of the pooling and the associated accounting hassles.