Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
<p>Abstract</p> <p>Background</p> <p>Massively 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 wit...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-11-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/572 |
| _version_ | 1818061048235687936 |
|---|---|
| author | Chen Zuozhou Miller Christopher A Yu Fuli Coarfa Cristian Harris R Alan Milosavljevic Aleksandar |
| author_facet | Chen Zuozhou Miller Christopher A Yu Fuli Coarfa Cristian Harris R Alan Milosavljevic Aleksandar |
| author_sort | Chen Zuozhou |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Massively 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.</p> <p>Results</p> <p>Pash 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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-10T13:42:07Z |
| format | Article |
| id | doaj.art-245ac91b21eb421eae64c56b4ff58722 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T13:42:07Z |
| publishDate | 2010-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-245ac91b21eb421eae64c56b4ff587222022-12-22T01:46:37ZengBMCBMC Bioinformatics1471-21052010-11-0111157210.1186/1471-2105-11-572Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencingChen ZuozhouMiller Christopher AYu FuliCoarfa CristianHarris R AlanMilosavljevic Aleksandar<p>Abstract</p> <p>Background</p> <p>Massively 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.</p> <p>Results</p> <p>Pash 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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/11/572 |
| spellingShingle | Chen Zuozhou Miller Christopher A Yu Fuli Coarfa Cristian Harris R Alan Milosavljevic Aleksandar Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing BMC Bioinformatics |
| title | Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing |
| title_full | Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing |
| title_fullStr | Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing |
| title_full_unstemmed | Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing |
| title_short | Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing |
| title_sort | pash 3 0 a versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel dna sequencing |
| url | http://www.biomedcentral.com/1471-2105/11/572 |
| work_keys_str_mv | AT chenzuozhou pash30aversatilesoftwarepackageforreadmappingandintegrativeanalysisofgenomicandepigenomicvariationusingmassivelyparalleldnasequencing AT millerchristophera pash30aversatilesoftwarepackageforreadmappingandintegrativeanalysisofgenomicandepigenomicvariationusingmassivelyparalleldnasequencing AT yufuli pash30aversatilesoftwarepackageforreadmappingandintegrativeanalysisofgenomicandepigenomicvariationusingmassivelyparalleldnasequencing AT coarfacristian pash30aversatilesoftwarepackageforreadmappingandintegrativeanalysisofgenomicandepigenomicvariationusingmassivelyparalleldnasequencing AT harrisralan pash30aversatilesoftwarepackageforreadmappingandintegrativeanalysisofgenomicandepigenomicvariationusingmassivelyparalleldnasequencing AT milosavljevicaleksandar pash30aversatilesoftwarepackageforreadmappingandintegrativeanalysisofgenomicandepigenomicvariationusingmassivelyparalleldnasequencing |