WASP2: Allele-Specific Analysis#

PyPI Tests

WASP2 is a comprehensive suite of tools for unbiased allele-specific analysis of next-generation sequencing data. It addresses reference bias in read mapping and provides statistical methods for detecting allelic imbalance.

Features#

  • Unbiased Mapping: WASP algorithm for correcting reference bias (van de Geijn et al. 2015, Nat Methods 10.1038/nmeth.3582)

  • Allele Counting: Count allele-specific reads from BAM files

  • Statistical Analysis: Beta-binomial likelihood-ratio tests for allelic imbalance

  • Single-Cell Support: Specialized tools for single-cell RNA-seq and scATAC-seq

  • Rust-Accelerated: Rust-backed BAM filtering and counting for large cohorts

Quick Start#

Install via pip:

pip install wasp2

Count alleles from a BAM file:

wasp2-count count-variants sample.bam variants.vcf

Analyze allelic imbalance:

wasp2-analyze find-imbalance counts.tsv

Documentation#

Getting Started

User Guide

Tutorials

Statistical Methods

API Reference

Development

Indices and tables#