This repository is moved to https://github.com/GeneDX/pgr-tk-notebooks/. Please check there for the latest update. This is archived only for crossreference purpose. Thanks.
Jupyter Notebooks Using PGR-TK for various human pangenome analysis tasks (see https://github.com/Sema4-Research/pgr-tk/blob/main/README.md)
00-0-setup.ipynb # optional setup for the computing environment
00-1-create_pgr_index.ipynb # note for creating the pgr-tk index
01-read_and_query_pgr-db_example.ipynb # simple sequence fetching and query example
02-KCNE1-MAPG_different_scales.ipynb # generating the KCNE1 MAP graphs
03-MHC-HLA.ipynb # generate the MHC HLA MAP graph in GFA format
04-AMY1A.ipynb # generate the AMY1A examples
05-0-Generate_CMRG_MAPG_sequences.ipynb # fetch and processing the CMRG
05-1-Partition_CMRG_sequence_dipcall.ipynb # generate alignment ofr the CMRG
06-Graph_Complexity.ipynb # compute the graph complexity metrics and the local repetitiveness
07-0-LPA.ipynb # LPA analysis
07-1-LPA-repeat.ipynb # LPA analysis for the repeats
07-2-LPA-just_repeat.ipynb # LPA analysis for the repeats with pre-generated files of the LPA sequences
08-0-DAZ1234.ipynb # DAZ1234 general analysis
08-1-DAZ1234-t2t-hg002-asm.ipynb # DAZ1234 analsysis with the t2t hg002 assembly
08-2-DAZ1234-all_at_once.ipynb # DAZ1234 analysis
09-KATNAL2.ipynb # KATNAL2 repeat analysis
10-MHC-HLA-II-GraphDecomposition.ipynb # MHC, principal graph decomposition
11-SMN12_repeat_region.ipynb # SMN1/2 region MAP graph
12-OPN1MW.ipynb
13-TSPY1.ipynb
14-RBMY.ipynb
15-GPRIN2.ipynb