Download All Data Files | Data description | Load packages | Data preparation | 01. Prepare data | 02. Process data. | Model inference | Explore all models | Model interpretation | Running only the best model | Bootstrap replicates

Preprocessing | Option 1: Reference genome | Align to a reference genome | Remove repeats | Identify repeat regions | Remove repeats from your alignment | Filter low quality | Option 2: Target-based | Data processing with nQuack | Step 1: Prepare. | Warning: samtools must be local! | Step 2: Process | When should you filter your data? | Coverage filters. | Allele Frequency | Comparing nQuack to nQuire | What about 'denoising'? | Alternative approach - Bclean | Bclean and Denoise

Can it go faster? | Should I subsample my data? | What about higher ploidal levels? | Can I identify if my sample is an allopolyploid or autopolyploid? | What about RNA-seq? HI-C? or PacBio HIFI?

Part 1: Data preparation | Load packages | Set up parallel | 01. Prepare data | 02. Process data. | Stop cluster | Part 2: Model inference | SLURM Example | 02_Model.R | What if I am not using SLURM? | Wait, this is still slow! | 02_Model_withTimers.R

Site-based heterozygosity | nQuack | Model types | Additional arguments. | Mixture model implementation. | Implementation | Interpretation

Simulate Data | Comparing the Log-Likelihood | TLDR

Introduction to Qploidy2 | Using data from Qploidy2 with nQuack | Predicting individual's ploidal level | Step 1: Modifying input from Qploidy2 to nQuack | Step 2: Model inference | Identify the most accurate model

Simple or Idealisitic | Advanced or Realistic

Load Packages | Read in your VCF file | Subset information from the Genotypes | 01. Subset total read depth | 02. Subset reference read depth and alternative read depth | 02A. Subset reference read depth | 02B. Subset alternative read depth | 03. Process for nQuack

Data Downloading | Identifying Synonyms | Download with gatoRs | Data Processing | Identify Records Missing Locality Information | Redacted Records | Records to Georeference | Merging Retained Records | Occurrence Data Cleaning | Resolve Taxon Names | Clean Locality | Basic Locality Clean | Find and Remove Flagged Points | Remove Duplicate Records | Remove Particular Record Bases | Spatial Correction | One Point Per Pixel | Spatial thining | Full Clean | Downstream Data Proccessing | Prepared data for MAXENT | Prepared data for publication

Download All Data Files | Data description | Load packages | Data preparation | 01. Prepare data | 02. Process data. | Model inference | Explore all models | Model interpretation | Running only the best model | Bootstrap replicates

Preprocessing | Option 1: Reference genome | Align to a reference genome | Remove repeats | Identify repeat regions | Remove repeats from your alignment | Filter low quality | Option 2: Target-based | Data processing with nQuack | Step 1: Prepare. | Warning: samtools must be local! | Step 2: Process | When should you filter your data? | Coverage filters. | Allele Frequency | Comparing nQuack to nQuire | What about 'denoising'? | Alternative approach - Bclean | Bclean and Denoise

Can it go faster? | Should I subsample my data? | What about higher ploidal levels? | Can I identify if my sample is an allopolyploid or autopolyploid? | What about RNA-seq? HI-C? or PacBio HIFI?

Introduction to Qploidy2 | Using data from Qploidy2 with nQuack | Predicting individual's ploidal level | Step 1: Modifying input from Qploidy2 to nQuack | Step 2: Model inference | Identify the most accurate model

Load Packages | Read in your VCF file | Subset information from the Genotypes | 01. Subset total read depth | 02. Subset reference read depth and alternative read depth | 02A. Subset reference read depth | 02B. Subset alternative read depth | 03. Process for nQuack

Part 1: Data preparation | Load packages | Set up parallel | 01. Prepare data | 02. Process data. | Stop cluster | Part 2: Model inference | SLURM Example | 02_Model.R | What if I am not using SLURM? | Wait, this is still slow! | 02_Model_withTimers.R

Site-based heterozygosity | nQuack | Model types | Additional arguments. | Mixture model implementation. | Implementation | Interpretation

Simple or Idealisitic | Advanced or Realistic

Simulate Data | Comparing the Log-Likelihood | TLDR

Retry Function | Use the Retry Function