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HIA: a genome mapper using hybrid index-based sequence alignment

Overview of attention for article published in Algorithms for Molecular Biology, January 2015
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2 tweeters

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16 Mendeley
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Title
HIA: a genome mapper using hybrid index-based sequence alignment
Published in
Algorithms for Molecular Biology, January 2015
DOI 10.1186/s13015-015-0062-4
Pubmed ID
Authors

Choi, Jongpill, Park, Kiejung, Cho, Seong Beom, Chung, Myungguen

Abstract

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools. HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table and suffix array (hybrid index) is much faster than the suffix array method for finding a substring in the reference sequence. Here, we defined the matching region (MR) is a longest common substring between a reference and a read. And, we also defined the candidate alignment regions (CARs) as a list of MRs that is close to each other. The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read. We found that aligning only the unmatched regions in the CAR is much faster than aligning the whole CAR. In benchmark analysis, HIA outperformed in mapping speed compared with the other aligners, without significant loss of mapping accuracy. Our experiments show that the hybrid of hash table and suffix array is useful in terms of speed for mapping NGS sequencing reads to the human reference genome sequence. In conclusion, our tool is appropriate for aligning massive data sets generated by NGS sequencing.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 16 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Korea, Republic of 1 6%
France 1 6%
Unknown 14 88%

Demographic breakdown

Readers by professional status Count As %
Researcher 7 44%
Student > Ph. D. Student 3 19%
Student > Master 2 13%
Lecturer 1 6%
Professor 1 6%
Other 1 6%
Unknown 1 6%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 31%
Computer Science 5 31%
Agricultural and Biological Sciences 3 19%
Medicine and Dentistry 1 6%
Unknown 2 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 January 2016.
All research outputs
#10,189,233
of 16,534,657 outputs
Outputs from Algorithms for Molecular Biology
#108
of 229 outputs
Outputs of similar age
#185,744
of 372,455 outputs
Outputs of similar age from Algorithms for Molecular Biology
#10
of 25 outputs
Altmetric has tracked 16,534,657 research outputs across all sources so far. This one is in the 36th percentile – i.e., 36% of other outputs scored the same or lower than it.
So far Altmetric has tracked 229 research outputs from this source. They receive a mean Attention Score of 2.9. This one is in the 47th percentile – i.e., 47% of its peers scored the same or lower than it.
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We're also able to compare this research output to 25 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.