Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Meraculous-2D: Haplotype-sensitive Assembly of Highly Heterozygous
  genomes   While many short read assemblers attempt to simplify the de Brujin graph by
identifying and resolving variant-induced bubbles to produce a haploid mosaic
result, this approach is only viable when variants are relatively rare and the
bubbles are well defined in a graph context. We observed that diploid genomes
with very high levels of heterozygosity fail to display well-resolved bubble
structures in a typical assembly graph and thus result in highly fragmented and
incomplete assemblies. Here we present an enhancement of Meraculous2 algorithm,
called Meraculous-2D, which preserves haplotypes across variant sites and
generates accurate assembly of highly heterozygous diploid genomes. Preserving
and taking advantage of the allelic variation throughout the assembly process
allows reconstructing both haplomes at once, without the need to pick arbitrary
paths through bubble structures. We also enhanced the original diploidy
resolution method of Meraculous2 to maintain and report phased haplotype
variant information.

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The categories of this paper are: chem-ph
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The categories of this paper are: q-alg
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The categories of this paper are: cs
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The categories of this paper are: funct-an
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The categories of this paper are: chao-dyn
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The categories of this paper are: comp-gas
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The categories of this paper are: hep-ex
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The categories of this paper are: dg-ga
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The categories of this paper are: cond-mat
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The categories of this paper are: solv-int
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The categories of this paper are: gr-qc
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The categories of this paper are: nlin
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The categories of this paper are: hep-th
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The categories of this paper are: mtrl-th
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The categories of this paper are: math
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The categories of this paper are: econ