Read Mapping Algorithms for Single Molecule Sequencing Data

Yanovsky, Vladimir; Rumble, Stephen M.; Brudno, Michael

doi:10.1007/978-3-540-87361-7_4

Cited by 5 publications

(3 citation statements)

References 13 publications

(24 reference statements)

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“…Within SHRiMP we have implemented separate final alignment modules for Illumina/Solexa data (this is done with the regular Smith-Waterman algorithm) and for color-space (di-base) data produced by the AB SOLiD instrument (described in the next section). Additionally we have an experimental module for alignment of two-pass sequencing data, where two reads are generated from every genomic location, which is described elsewhere [20] .…”

Section: Resultsmentioning

confidence: 99%

SHRiMP: Accurate Mapping of Short Color-space Reads

et al. 2009

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The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25–70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits. We use SHRiMP to map reads from a newly sequenced Ciona savignyi individual to the reference genome. We demonstrate that SHRiMP can accurately map reads to this highly polymorphic genome, while confirming high heterozygosity of C. savignyi in this second individual. SHRiMP is freely available at http://compbio.cs.toronto.edu/shrimp.

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Section: Resultsmentioning

confidence: 99%

SHRiMP: Accurate Mapping of Short Color-space Reads

et al. 2009

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“…Gene ontology data analysis was performed using PANTHER (version 7.0) database [45] . We have analyzed the biological processes of the hotspots genes ( Information S1 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans

et al. 2011

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The primary objective of this study was to create a genome-wide high resolution map (i.e., >100 bp) of ‘rearrangement hotspots’ which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs) into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a ‘seed and extend’ approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (18× coverage), including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs). These regions are correlated with increased non-allelic homologous recombination (NAHR) event frequency which presumably represents the origin of copy number variations (CNVs) and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of ‘rearrangement hotspots’, which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s) for development of constitutional and acquired diseases.

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“…et al , 2008 ; Li,R. et al , 2008 ; Lin et al , 2008 ; Schatz, 2009 ; Yanovsky et al , 2008 ), with improvements in both efficiency and breadth of functionality (e.g. ability to map paired-end reads; integrated SNP calling).…”

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Updates to the RMAP short-read mapping software

et al. 2009

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Summary: We report on a major new version of the RMAP software for mapping reads from short-read sequencing technology. General improvements to accuracy and space requirements are included, along with novel functionality. Included in the RMAP software package are tools for mapping paired-end reads, mapping using more sophisticated use of quality scores, collecting ambiguous mapping locations and mapping bisulfite-treated reads.Availability: The applications described in this note are available for download at http://www.cmb.usc.edu/people/andrewds/rmap and are distributed as Open Source software under the GPLv3.0. The software has been tested on Linux and OS X platforms.Contact: andrewds@usc.edu; mzhang@cshl.eduThe RMAP algorithm was introduced by (Smith et al., 2008) as one of the earliest available programs for mapping reads from the Illumina second-generation sequencing technology. One important contribution of RMAP was to incorporate the use of quality scores directly into the mapping process: read positions with too low a quality score were not considered while mapping, and that quality score cutoff could be adjusted by the user. Subsequently, numerous mapping algorithm have appeared (Langmead et al., 2009; Li,H. et al., 2008; Li,R. et al., 2008; Lin et al., 2008; Schatz, 2009; Yanovsky et al., 2008), with improvements in both efficiency and breadth of functionality (e.g. ability to map paired-end reads; integrated SNP calling). Investigators requiring solutions to mapping problems now have many options. As new applications of short-read sequencing emerge, many variations on the analysis task of read mapping emerge. Diversity in performance characteristics of existing mapping tools becomes potentially valuable.We report the first major update to RMAP. The basic algorithmic framework in RMAP is still to preprocess reads and scan the genome, but several modifications have been made and much additional functionality has been included. Importantly, RMAP has a memory footprint that depends on the number of reads being mapped. This feature allows RMAP to be used effectively in cluster environments with commodity nodes, because partitioning the reads allows natural parallelizations with linear reduction in memory requirements per processor core used.Included in this release of the RMAP software package is functionality for mapping paired-end reads, making more sophisticated use of quality scores, collecting mapping locations for ambiguously mapping reads and mapping bisulfite-treated reads.

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Read Mapping Algorithms for Single Molecule Sequencing Data

Cited by 5 publications

References 13 publications

SHRiMP: Accurate Mapping of Short Color-space Reads

SHRiMP: Accurate Mapping of Short Color-space Reads

Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans

Updates to the RMAP short-read mapping software

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