hannesbecher / shiny-k-mers
Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
☆13Updated 5 months ago
Alternatives and similar repositories for shiny-k-mers:
Users that are interested in shiny-k-mers are comparing it to the libraries listed below
- ☆19Updated 3 months ago
- A genome-wide IM blockwise likelihood estimation toolkit☆15Updated 7 months ago
- Biodiversity Genomics Academy 2023: Understanding k-mers and ploidy using Smudgeplot☆10Updated last year
- Reference genome quality scores☆19Updated 4 years ago
- Sampling and inference of genealogies with recombination☆29Updated 4 months ago
- A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.☆11Updated 11 months ago
- Estimating repeat spectra and genome length from low-coverage genome skims☆11Updated last year
- 🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling☆27Updated last year
- The powerful `awk` script to calculate pi, Dxy and Fst in polyploid VCF files with mixed-ploidy groups support☆24Updated last month
- The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequ…☆38Updated last year
- Minimizer-based assembly scaffolding and mapping using long reads☆35Updated 3 months ago
- Framework for analyzing low depth NGS data in heterogeneous populations using PCA.☆48Updated this week
- Code and binaries related to processing haplotagging data☆13Updated 2 years ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆13Updated 2 years ago
- ☆11Updated 5 years ago
- convert PAF format to CHAIN format☆26Updated last month
- Software for detecting introgression using supervised machine learning☆18Updated 2 years ago
- Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.☆15Updated this week
- A tool for the recovery of unassembled telomeres from soft-clipped read alignments.☆35Updated last month
- Genetic Map Comparison☆20Updated 2 years ago
- assembly evaluation tool☆34Updated 2 years ago
- heterozygosity-based estimator of Rho - https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac100/6623412☆10Updated last year
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆31Updated 2 years ago
- A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models☆17Updated 2 years ago
- CoalHMM☆22Updated 11 years ago
- Scripts for reformatting data. Mainly from tab separated to an esoteric program specific format☆13Updated last week
- ☆17Updated 7 years ago
- ✏️ Genome assembly polishing & SNV detection☆64Updated last month
- The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).☆20Updated 3 years ago