The analysis scripts used in four Papaver genome centromere satellites analysis projects.
There are 13 scripts, and the introduction and description as following:
1_buildingSatellites.sh the script used to build satellite library
2_processTRFforlastz.py the script used to filter TRF results to get tandem repeat regions
3_filterNamelist.py the script used to filter the TRF overlapping results
4_splitNamelist.py the script used to split the files for parallel
5.1_runSD_batch.sh the script used to run StringDecomposer
5.2_checkSD.py the script used to checke the StringDecomposer results
6_getSDContinueRegion.py the script used to obtain the continues regions from StringDecomposer results
7_run_batch_lastz.sh the script used to run lastZ
8_run_batch_edge.sh the script used to get the edges between satellites
9_mergeEdge.py the script used to merge the edges for final edge list
10_buildSatellates.py the script used to obtain satellites and name them, like Prh168S1
11_panLastz.py the script used to obtain the satellites shared in multip-species
12_panEdge.py the script used to construct edge list of cross species satellites
13_getLastzRegion.py the script used to obtain the lastZ alignment regions given a specific satellite