Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. Conclusions: We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.
References in zbMATH (referenced in 1 article )
Showing result 1 of 1.
- Shen, Carol; Shen, Tony; Lin, Jimmy: Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future (2017)