deletions | additions       diff --git a/Library Preparation and Sequencing .md b/Library Preparation and Sequencing .md  index e5f1008..af012db 100644  --- a/Library Preparation and Sequencing .md  +++ b/Library Preparation and Sequencing .md 
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Given the overcapacity of Illumina sequencing for bacterial genomes, 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 accounting hassles. However, collaborating with other groups can be a great option. Many labs sequence genomes or metageomes on a regular basis; adding in one additional sample isn't technically very difficult, but it will entail oversight of the pooling and the associated accounting hassles. This will also entail a discussion of barcode compatibility, to ensure that all barcodes are sufficiently unique for demultiplexing.  ##Downsampling  Coverage (read depth) is the average number of reads representing a given nucleotide and is a function of the number and size of genomes pooled onto a run. The optimal amount of coverage depends on the read length, the assembler being used, and other factors. For Illumina data assembled using this workflow we recommend that this number be between 20x and 200x. See our more detailed discussion in section ??? "Interpretation of A5-miseq stats". If you have coverage significantly higher than 200x and wish to downsample your data we have written a script(sub_sample_reads)  (sub\_sample\_reads) for this purpose. You will first need to calculate how many reads you want the script to sample. We recommend determining how many reads would be equivalent to 100x coverage (divide the genome size by the average read length and multiply by 100). You can download the script using from  the curl command. figshare zipped script file (http://figshare.com/articles/Miscellaneous_Scripts_for_Workflow/1086285).  Create a new directory containing the script (sub\_sample\_reads) and the  reads you wish to downsample.In the terminal navigate the directory you just created and download the script using the following syntax   curl https://raw.githubusercontent.com/gjospin/scripts/master/subsample_reads.pl > sub_sample_reads.pl    To downsample the data navigate to the directory you just created (in the terminal) and  use the following command /sub_sample_reads file1 file2 #_reads_to_keep output_file_name   for example