PASH

PASH maps short and long sequencing reads and performs sequence comparison for genome-wide analyses, including ChIP-seq and methylome mapping using whole-genome bisulfite sequencing.

Key Features:

• Read mapping (short and long reads): Maps both short and long reads produced by massively parallel sequencing and matches or exceeds niche programs for short-read accuracy while demonstrating superior performance for longer reads.
• Gapped k-mer alignment: Implements a gapped k-mer alignment method that does not rely on seed-based comparison techniques.
• Multi-positional hash tables: Employs multi-positional hash tables to facilitate alignment and mapping.
• Indel and repetitive-region mapping: Effectively maps genomic regions rich in repetitive elements and polymorphic sites, including indel polymorphisms.
• Bisulfite sequencing support: Supports methylome mapping from whole-genome bisulfite sequencing and whole-genome shotgun bisulfite sequencing datasets.
• Pipeline integration: Operates as a module within configurable analysis pipelines for tasks such as ChIP-seq.
• Hardware scalability: Maintains performance across individual computers with standard RAM, multi-core architectures, and large computational clusters.

Scientific Applications:

• ChIP-seq analysis: Mapping reads for ChIP-seq experiments to support genome-wide protein–DNA interaction studies.
• Methylome mapping and CpG analysis: Mapping whole-genome (shotgun) bisulfite sequencing reads to analyze CpG methylation, CpG SNPs, and genomic imprinting.
• Genetic and epigenetic variation studies: Genome-wide analyses of polymorphic sites, indels, and epigenomic variation.

Methodology:

PASH implements a gapped k-mer alignment method that eschews seed-based comparisons and employs multi-positional hash tables to map short and long reads, accommodating indel polymorphisms from massively parallel sequencing data.