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benchNGS : An approach to benchmark short reads alignment tools

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Paper breakdownThe authors' claims, conditions and measurements, as JSON Signed receiptProof this review has not been altered
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Farzana Rahman, Mehedi Hassan, Alona Kryshchenko, Inna Dubchak, Tatiana V. Tatarinova, Nickolai Alexandrov

Genomics · Submitted 24 Apr 2015

abstract compiled · 2026-09-23 · no language-model review

The authors' main claim In this paper we propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences.

how it is stated · asserted 0.94 read the record →

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arXiv ID1504.06659 (version 1)
Pith IDBVO235Q2, Pith's permanent record of this paper and its review
CitationAlona Kryshchenko, Farzana Rahman, Inna Dubchak, Mehedi Hassan, Nickolai Alexandrov, Tatiana V. Tatarinova. "benchNGS : An approach to benchmark short reads alignment tools." arXiv:1504.06659 (2015). https://pith.science/paper/BVO235Q2
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The compiled record

The paper's own sentences, arranged. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.

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Compiled by classifier-1.13-20260917 via OpenRouter, question bank abstract-p1-20260923, 2026-09-23: 1 request, 4,264 input tokens, $0.0002 reported.

What the abstract itself states, as probabilities: claims first 0.05 · states limitation 0.11 · human participants 0.03 · controlled comparison 0.42 · randomized assignment 0.01 · states quantitative result 0.53 · compares with prior results 0.50 · mentions code or data availability 0.04.

The abstract, sentence by sentence

arXiv listing abstract v1. Results and the main claim are underlined; .

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when the NGS reads are quite different from the available reference genome. We propose a benchmark to assess accuracy of short reads mapping based on the pre-computed global alignment of related genome sequences. In this paper we propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. We outline the method and also present a short report of an experiment performed on five popular alignment tools based on the pairwise alignments of Escherichia coli O6 CFT073 genome with genomes of seven other bacteria.

background contribution method result interpretation main claim

What the classifier reports for each sentence. The number is the probability it gave the label.
#sentencerolethe authors' own workstates the main conclusionstrength
s0 In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. background 1.00 0.04 0.02 asserted 1.00
s1 The accuracy of these programs may vary significantly, especially when the NGS reads are quite different from the available reference genome. background 0.93 0.07 0.03 hedged possibility 1.00
s2 We propose a benchmark to assess accuracy of short reads mapping based on the pre-computed global alignment of related genome sequences. contribution 0.99 0.78 0.26 asserted 0.93
s3 In this paper we propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. contribution 0.99 0.82 0.20 asserted 0.94
s4 We outline the method and also present a short report of an experiment performed on five popular alignment tools based on the pairwise alignments of Escherichia coli O6 CFT073 genome with genomes of seven other bacteria. contribution 0.50 0.95 0.10 asserted 0.99

What kind of paper the classifier reports this is: dataset or benchmark 0.94 · evidence from observation or experiment 0.83.

What was examined, and what was not

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  • full text
  • figures and tables
  • references and citing sentences
  • relations to other papers
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  • P abstract
not run
  • S sections
  • T body sentences
  • C citations
  • R cross-paper relations

Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

The paper
Original abstract

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when the NGS reads are quite different from the available reference genome. We propose a benchmark to assess accuracy of short reads mapping based on the pre-computed global alignment of related genome sequences. In this paper we propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. We outline the method and also present a short report of an experiment performed on five popular alignment tools based on the pairwise alignments of Escherichia coli O6 CFT073 genome with genomes of seven other bacteria.

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