This contains scripts which implement the analysis described in the Methods
of Ewing and Kazazian 2010. This implementation assumes a computing cluster 
running SGE, and must be customized depending on the filesystem structure, 
maximum queue length, database configuration, etc. Please contact 
aewing4@jhmi.edu for assistance should you choose to use this particular 
implementation. Scripts in this directory are started using run_continuous.sh 
and assume per-individual directories containing fastq files which follow the 
naming  conventions used by the 1000 Genomes Project working group. A list of 
these directories should be put into a file which is used as an arguement to
run_continuous.sh. Following this, the output files should be dumped into a
single file for each individual and moved to the database directory for 
further processing. Once the L1-genome paired reads are in a suitable table, 
the script 'buildpeaks.pl' builds 'peaks' from the genomic locations of these 
reads as described in the paper. Following this, the script 'findinsertions.pl'
is used to identify L1 insertions from the table generated by 'buildpeaks.pl'.
