2012
DOI: 10.1186/1471-2105-13-189
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AGORA: Assembly Guided by Optical Restriction Alignment

Abstract: Background: Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs). Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. Howe… Show more

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Cited by 45 publications
(34 citation statements)
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“…It has been applied to the maize and the rice genome [11], [21]. One can validate a sequence assembly by comparing in silico sequence motif maps to consensus optical maps [22][25]. However, information density for optical maps is only about one site per 20 kb, and the technology is limited in utility by high error-rates, non-uniform DNA linearization, and low throughput.…”
Section: Introductionmentioning
confidence: 99%
“…It has been applied to the maize and the rice genome [11], [21]. One can validate a sequence assembly by comparing in silico sequence motif maps to consensus optical maps [22][25]. However, information density for optical maps is only about one site per 20 kb, and the technology is limited in utility by high error-rates, non-uniform DNA linearization, and low throughput.…”
Section: Introductionmentioning
confidence: 99%
“…Additionally, our current assembly approach is not fully integrated; sequence contigs and genome maps are separately assembled before scaffolding. Integrated methods such as AGORA have been restricted to genomes with single complete genome maps or to simple bacterial genomes but could potentially lead to better anchoring of sequence contigs within scaffolds, better N50 values 39 and better haplotype resolution (by extending existing string graph algorithms, which have the potential to directly reconstruct de novo haplotypes from sequencing data) 40 . Such approaches could obviate mapping-based SV detection, especially in the context of large SVs.…”
Section: Discussionmentioning
confidence: 99%
“…Map-generating technologies pioneered by BioNano Genomics, the Irys System, use rare-cut genomic DNA subjected to electrophoretic current to produce physical maps as well (38, 39). Physical or optical mapping methods can be used to improve graph navigation (40), to validate chromosomal ordering of contigs, and to detect and break up chimeric contigs. Random fosmid sequencing was also used as a kind of physical map for evaluation in Assemblathon 2.…”
Section: Evaluating Genome Assembliesmentioning
confidence: 99%