GeIST version 2.1.0

Changes:

• The sequence input can now be either a BAM file or a FASTQ file. If using a BAM file, make sure that BamTools is installed on your system.
• All input files can now be specified by absolute or relative paths, and don't need to be in the GeIST directory.

GeIST version 2.0.0

The following changes distinguish GeIST v2.0.0 from the version used in LaFave et al. 2014 (http://dx.doi.org/10.1093/nar/gkt1399). The version used for that paper can be found at http://research.nhgri.nih.gov/software/GeIST/download.shtml.

• GeIST 2.0.0 can be used to identify AAV, Tol2, and Ac/Ds integrations, in addition to MLV.
• Input is now entered via command line options, rather than specifying the input files in a specific order
• GeIST now uses a more detailed barcode file that allows the user to associate barcodes and group numbers with plate/well position, group name (such as the ID of a transgenic line), and individual sample ID
• Now capable of running on OS X, in addition to Linux
• Required overlap for cutadapt trimming steps has been adjusted to be more conservative, which should help avoid false positives in as many as 400 million reads
• The filtering of putative false positives within 5 bp of a site with a higher integration count in the same group is now strand-aware
• For purposes of calculating the number of independent integrations in the same site, GeIST no longer assumes the samples have undergone at most one round of DNA replication
• The default Bowtie output has been replaced with SAM/BAM output