GeneDx / pgr-tk-notebooks
Jupyter Notebooks Using PGR-TK for various human pangenome analysis tasks
☆14Updated last year
Alternatives and similar repositories for pgr-tk-notebooks:
Users that are interested in pgr-tk-notebooks are comparing it to the libraries listed below
- ☆14Updated 9 months ago
- Genome Assembly 102☆13Updated this week
- SV calling for diploid assemblies☆23Updated 9 months ago
- ☆31Updated 5 years ago
- A module for improving the insertion sequences of structural variant calls☆30Updated 3 years ago
- TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain☆20Updated 7 months ago
- Kmer based genotyper for short reads.☆23Updated 3 years ago
- somatic SV calling on matched tumor-normal co-assembly graphs☆18Updated 5 months ago
- Identification of segmental duplications in the genome☆26Updated 2 years ago
- Integrate multiple genome assemblies into a pangenome graph☆32Updated 2 years ago
- A Hi-C scaffolding method☆22Updated 3 years ago
- building a human pangenome from the HPRCy1v2 genbank accessioned assemblies☆14Updated last year
- Very simple and configurable all-in-one dotplot program☆12Updated last year
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆29Updated last month
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Updated 6 years ago
- Genotyping of segregating mobile elements insertions☆19Updated 3 years ago
- PGR-TK: Pangenome Research Tool Kit☆12Updated last month
- Scripts used to perform analyses in Rice et al. (2023)☆15Updated last year
- Invertory of TE-gene isoforms☆9Updated last year
- Convert RepeatMasker ".out" file into a gff3 with colors!!!☆20Updated 4 years ago
- R package and wrapper functions for identifying serial structural variations from genome assemblies☆26Updated 3 months ago
- Construct and Analyze the North American Vitis pangenome☆21Updated last year
- An algorithm for centromere assembly using long error-prone reads☆26Updated 3 years ago
- Kmer Analysis of Pileups for Genotyping☆21Updated 2 weeks ago
- Plant genome assembly and annotation pipeline using snakemake☆35Updated last year
- use variant nesting information to flter overlapping sites from vg deconstruct output☆26Updated 6 months ago
- ☆15Updated 2 years ago
- Phase reads, assemble haplotypes and detect SVs☆19Updated 4 years ago
- Computational Pangenomics☆17Updated 2 years ago
- Method to optimally select samples for validation and resequencing☆27Updated 3 years ago