Limits...
ALLMAPS: robust scaffold ordering based on multiple maps.

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J - Genome Biol. (2015)

Bottom Line: The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly.Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies.ALLMAPS is a useful tool in building high-quality genome assemblies.

View Article: PubMed Central - PubMed

Affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. tanghaibao@gmail.com.

ABSTRACT
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS .

Show MeSH

Related in: MedlinePlus

Integration of various mapping evidence inside the ALLMAPS framework. (A) Various map types converted to a ‘coordinate-based’ generic marker type that allows universal treatment. (B) Example from Medicago to demonstrate ALLMAPS input BED format. Markers derived from genetic map, optical map, and comparative map are highlighted in different colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4305236&req=5

Fig3: Integration of various mapping evidence inside the ALLMAPS framework. (A) Various map types converted to a ‘coordinate-based’ generic marker type that allows universal treatment. (B) Example from Medicago to demonstrate ALLMAPS input BED format. Markers derived from genetic map, optical map, and comparative map are highlighted in different colors.

Mentions: After applying ALLMAPS to multiple genetic maps, we further highlight ALLMAPS’s ability to go beyond genetic maps to use other types of genomic maps. A combination of several independent lines of evidence will further complement each other in different regions of the genome. There are specialized methods for handling different mapping data individually, including tools for optical map alignment [9,12] and synteny-guided assembly [4,13], but these methods were never combined within the same framework to exploit multiple maps. One obstacle is that other genomic maps may require some data transformation before being imported into ALLMAPS. We note that a generalized form of genomic maps is constituted by markers represented as (x, y) - each marker having a coordinate on the genomic scaffolds (x) and another coordinate on the map (y), respectively. As long as the map can be converted into a list of abstract ‘markers’ carrying these two coordinates (in a standard BED format), they can be easily integrated in a unified framework (Figure 3). Details of this format and tools to transform data from optical map alignments and synteny alignments are available with the distribution of ALLMAPS: [30].Figure 3


ALLMAPS: robust scaffold ordering based on multiple maps.

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J - Genome Biol. (2015)

Integration of various mapping evidence inside the ALLMAPS framework. (A) Various map types converted to a ‘coordinate-based’ generic marker type that allows universal treatment. (B) Example from Medicago to demonstrate ALLMAPS input BED format. Markers derived from genetic map, optical map, and comparative map are highlighted in different colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4305236&req=5

Fig3: Integration of various mapping evidence inside the ALLMAPS framework. (A) Various map types converted to a ‘coordinate-based’ generic marker type that allows universal treatment. (B) Example from Medicago to demonstrate ALLMAPS input BED format. Markers derived from genetic map, optical map, and comparative map are highlighted in different colors.
Mentions: After applying ALLMAPS to multiple genetic maps, we further highlight ALLMAPS’s ability to go beyond genetic maps to use other types of genomic maps. A combination of several independent lines of evidence will further complement each other in different regions of the genome. There are specialized methods for handling different mapping data individually, including tools for optical map alignment [9,12] and synteny-guided assembly [4,13], but these methods were never combined within the same framework to exploit multiple maps. One obstacle is that other genomic maps may require some data transformation before being imported into ALLMAPS. We note that a generalized form of genomic maps is constituted by markers represented as (x, y) - each marker having a coordinate on the genomic scaffolds (x) and another coordinate on the map (y), respectively. As long as the map can be converted into a list of abstract ‘markers’ carrying these two coordinates (in a standard BED format), they can be easily integrated in a unified framework (Figure 3). Details of this format and tools to transform data from optical map alignments and synteny alignments are available with the distribution of ALLMAPS: [30].Figure 3

Bottom Line: The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly.Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies.ALLMAPS is a useful tool in building high-quality genome assemblies.

View Article: PubMed Central - PubMed

Affiliation: Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. tanghaibao@gmail.com.

ABSTRACT
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS .

Show MeSH
Related in: MedlinePlus