ArticleBMC bioinformatics2010
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.Nucleic acids research · 2025Article
- methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.Nucleic acids research · 2025Article
- Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.Computational and structural biotechnology journal · 2022Article
- Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues.Epigenetics · 2020Article
- DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis.Clinical epigenetics · 2019Review
- BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data.BMC bioinformatics · 2018Article
- Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.Science (New York, N.Y.) · 2018Article
- A new parallel pipeline for DNA methylation analysis of long reads datasets.BMC bioinformatics · 2017Article
- Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data.Briefings in bioinformatics · 2016Article
- Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations.Genome biology · 2016Article
- Integrating Epigenomics into the Understanding of Biomedical Insight.Bioinformatics and biology insights · 2016Review
- Article
- miR-137 Targets p160 Steroid Receptor Coactivators SRC1, SRC2, and SRC3 and Inhibits Cell Proliferation.Molecular endocrinology (Baltimore, Md.) · 2015Article
- Article
- Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.Nature communications · 2015Article
- HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples.Cancer informatics · 2015Article
- Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.Nucleic acids research · 2014Article
- CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma.PLoS genetics · 2014Article
- ARYANA: Aligning Reads by Yet Another Approach.BMC bioinformatics · 2014Article
- Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundMassively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.
resultsPash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms.
conclusionsWe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.