cschin / dash13-kir-mhc-assemblies

Repository for code and small data set for Dash13 Hackathon

dash13-KIR-MHC-assemblies

data source: 48.fastq.tar.gz shared by Marting from Dropbox

prefected data from HPRC:

data/HLA-ClassII_seq.fa.gz              # The HPRC HLA ClassII sequence file used in the paper
data/KIR_HPRC.000.fa                    # the HPRC KIR sequence file
data/KIR_example_seq_for_fetch.fa       # the sequence used for fetching for the KIR region

KIR resuls:

results/KIR/assemble_results.bed        # the principal bundle decomposition 
results/KIR/assemble_results.fa.gz      # the assembled sequence from the targeted sequence reads, 48.fastq.tar.gz
results/KIR/assemble_results.html       # the visualization of the principal bundle decomposition of the KIR region

Scripts:

scripts/run_hifiasm.sh                  # the example to sub-sampling and run hifiasm for assembling the targeted reads
scripts/run_pg_asm.sh                   # the example running Peregrine2021 to assemble the targeted reads
scripts/build_pbd.sh                    # the example to use PGR-TK to process the KIR pangenome

Proposed projects:

1. Using miniprop to align protein sequences on the pan-KIR sequences
2. Using LLM / ML techniques to classify the pan-KIR sequences
3. Imputation missing sequenceand genotype additional read eata with known haplotype sequence combinations

Reference:

• Paper: Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes: https://www.nature.com/articles/s41592-023-01914-y

• Other examples: https://github.com/GeneDx/pgr-tk-notebooks/

• The PGR-TK code: https://github.com/genedx/pgr-tk and https://github.com/cschin/pgr-tk

• protein sequences ftp://ftp.dfci.harvard.edu/pub/hli/tmp/pangene-primate-20230811.tar

• minprop: https://github.com/lh3/miniprot.git

• Immuannot: https://github.com/YingZhou001/Immuannot.git

• py-gfe: https://github.com/nmdp-bioinformatics/py-gfe

• GFE service: https://github.com/nmdp-bioinformatics/gfe-service

• https://hub.docker.com/r/nmdpbioinformatics/imgt_biosqldb/

• https://hub.docker.com/r/nmdpbioinformatics/gfe-db/