Abstract:
In genome/transcriptome assembly and similar scenarios, we are usually given millions of fragments and ready to assemble them into longer contigs by first aligning them t...Show MoreMetadata
Abstract:
In genome/transcriptome assembly and similar scenarios, we are usually given millions of fragments and ready to assemble them into longer contigs by first aligning them to a reference sequence. Since one fragment may be aligned to different locations due to sequence repetition, mutation, and artificial factors the alignment tools concern, users of alignment tools must make their own strategies for choosing one location for each fragment. Commonly used strategies usually assign the same value for each location or assign values according to alignment scores without taking into account the optimization. Considering that a reasonable strategy should ensure that the coverage at each base is similar, we depict the problem of assigning fragments to properly aligned positions as an optimization problem that minimizes the maximum coverage over all bases, studying the computational complexities for some cases and designing polynomial-time or approximate polynomial-time algorithms for them and some others.
Date of Conference: 05-08 December 2023
Date Added to IEEE Xplore: 18 January 2024
ISBN Information: