ALLMAPS: robust scaffold ordering based on multiple maps
By Haibao Tang, Xingtan Zhang, Chenyong Miao, Jisen Zhang, R. Ming, James c. Schnable, Patrick S. Schnable, E. Lyons, Jian-guo Lu. Genome Biology, 2015
364 citations recorded by the source corpus.
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.
Subfields: Artificial Intelligence, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/8310b75ec9cfde6139129a1dbd00cdde86c02f1f
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
In Plant Science
Citations in the corpus
- Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, neutral): “Genome assembly can also be greatly improved using genetic mapping populations to create a linkage map (Fierst 2015) and/ or through optical mapping that places scaffolds on chromosomes (Sharma et al. 2013; Tang et al. 2015 a , 2015 b ; VanBuren et al. 2015).”
- JCVI: A versatile toolkit for comparative genomics analysis (2024, methodology): “ALLMAPS (within the “ assembly.allmaps ” module) computes scaffold orders that maximize collinearity with a collection of maps, including genetic, physical, or comparative maps, thereby improving the accuracy and integrity of chromosomal assemblies [24].”