# Home

Harpy is a haplotagging data processing pipeline for Linux-based systems. It uses all the magic of Snakemake under the hood to handle the worklfow decision-making, but as a user, you just interact with it like a normal command-line program. Harpy uses both well known and niche programs to take raw haplotagging sequences and process them to become called SNP genotypes (or haplotypes) or large structural variants (inversions, deletions, duplications). Most of the settings are pre-configured and the settings you can modify are done at the command line.

# Harpy Modules

Harpy is modular, meaning you can use different parts of it independent from each other. Need to only align reads? Great! Only want to call variants? Awesome! All modules are called by harpy <workflow>. For example, use harpy align to align reads.

Workflow	Description
align	Align sample sequences to a reference genome
assembly	Create a genome assembly from linked-reads
demultiplex	Demultiplex haplotagged FASTQ files
impute	Impute genotypes using variants and sequences
metassembly	Create a metagenome assembly from linked-reads
phase	Phase SNPs into haplotypes
preflight	Run various format checks for FASTQ and BAM files
qc	Remove adapters, deduplicate, and quality trim sequences
simulate	Simulate haplotag linked reads or genomic variants
snp	Call SNPs and small indels
sv	Call large structural variants (inversions, deletions, duplications)

# Using Harpy

You can call harpy without any arguments (or with --help) to print the docstring to your terminal. You can likewise call any of the modules without arguments or with --help to see their usage (e.g. harpy align --help).

harpy --help
 Usage: harpy COMMAND [ARGS]...                                            
                                                                           
 An automated workflow for haplotagging linked-read data to go from raw    
 data to genotypes (or phased haplotypes). Batteries included.             
 demultiplex >> qc >> align >> snp >> impute >> phase >> sv                
                                                                           
 Documentation: https://pdimens.github.io/harpy/                           
                                                                           
╭─ Options ───────────────────────────────────────────────────────────────╮
│ --version      Show the version and exit.                               │
│ --help     -h  Show this message and exit.                              │
╰─────────────────────────────────────────────────────────────────────────╯
╭─ workflows ─────────────────────────────────────────────────────────────╮
│ demultiplex  Demultiplex haplotagged FASTQ files                        │
│ qc           Remove adapters and quality-control sequences              │
│ align        Align sample sequences to a reference genome               │
│ snp          Call SNPs and small indels on alignments                   │
│ sv           Call large structural variants on alignments               │
│ impute       Impute genotypes using variants and alignments             │
│ phase        Phase SNPs into haplotypes                                 │
│ simulate     Simulate variants or linked-reads from a genome            │
│ assembly     Create an assembly from linked-reads                       │
│ metassembly  Create a metassembly from linked-reads                     │
╰─────────────────────────────────────────────────────────────────────────╯
╭─ Other Commands ────────────────────────────────────────────────────────╮
│ resume        Resume a workflow from an existing Harpy directory        │
│ hpc           Profile templates for cluster job submissions             │
│ preflight     File format checks for haplotag data                      │
│ deconvolve    Resolve clashing barcodes from different molecules        │
│ popgroup      Create a template grouping file for samples               │
│ stitchparams  Create a template STITCH parameter file                   │
╰─────────────────────────────────────────────────────────────────────────╯

# Typical Linked-Read Workflows

Depending on your project goals, you may want any combination of SNPs, structural variants (inversions, deletions, duplications), or phased haplotypes. Below is a flow chart outlining a general workflow of linked-read data.

graph LR
    Demux([demultiplex]):::clean--->QC([QC, trim adapters, etc.]):::clean
    QC--->Align([align sequences]):::clean
    Align--->SNP([call SNPs]):::clean
    SNP--->Impute([impute genotypes]):::clean
    SNP--->Phase([phase haplotypes]):::clean
    Align--->SV([call structural variants]):::clean

    classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px

Alternatively, if you are interested in assembling a genome or metagenome, your workflow might look like:

graph LR
    QC([QC, trim adapters, etc.]):::clean--->DC([barcode deconvolution]):::clean
    DC--->Assembly([assembly/metassembly]):::clean

    classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px