Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Bermuda: Bidirectional de novo assembly of transcripts with new insights
  for handling uneven coverage   Motivation: RNA-seq has made feasible the analysis of a whole set of
expressed mRNAs. Mapping-based assembly of RNA-seq reads sometimes is
infeasible due to lack of high-quality references. However, de novo assembly is
very challenging due to uneven expression levels among transcripts and also the
read coverage variation within a single transcript. Existing methods either
apply de Bruijn graphs of single-sized k-mers to assemble the full set of
transcripts, or conduct multiple runs of assembly, but still apply graphs of
single-sized k-mers at each run. However, a single k-mer size is not suitable
for all the regions of the transcripts with varied coverage. Contribution: This
paper presents a de novo assembler Bermuda with new insights for handling
uneven coverage. Opposed to existing methods that use a single k-mer size for
all the transcripts in each run of assembly, Bermuda self-adaptively uses a few
k-mer sizes to assemble different regions of a single transcript according to
their local coverage. As such, Bermuda can deal with uneven expression levels
and coverage not only among transcripts, but also within a single transcript.
Extensive tests show that Bermuda outperforms popular de novo assemblers in
reconstructing unevenly-expressed transcripts with longer length, better
contiguity and lower redundancy. Further, Bermuda is computationally efficient
with moderate memory consumption.

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The categories of this paper are: atom-ph
5
The categories of this paper are: gr-qc
37
The categories of this paper are: supr-con
0
The categories of this paper are: hep-ph
20
The categories of this paper are: acc-phys
1
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: ao-sci
17
The categories of this paper are: q-fin
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The categories of this paper are: plasm-ph
9
The categories of this paper are: nlin
18
The categories of this paper are: econ
4
The categories of this paper are: cond-mat
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The categories of this paper are: eess
21
The categories of this paper are: adap-org
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The categories of this paper are: bayes-an