AdvISER-PYRO: amplicon identification using SparsE representation of PYROsequencing signal

J. Ambroise; A.S. Piette; C. Delcorps; L. Rigouts; B.C. de Jong; L. Irenge; A. Robert; J.L. Gala

doi:10.1093/bioinformatics/btt339

AdvISER-PYRO: amplicon identification using SparsE representation of PYROsequencing signal

J. Ambroise
, A.S. Piette
, C. Delcorps
, L. Rigouts
, B.C. de Jong
, L. Irenge
, A. Robert
, J.L. Gala

Mycobacteriology

Research output: Contribution to journal › A1: Peer-reviewed journal articles › peer-review

Abstract

Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights <5) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.

Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).

Original language	English
Journal	Bioinformatics
Volume	29
Issue number	16
Pages (from-to)	1963-1969
Number of pages	7
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btt339
Publication status	Published - 2013

Keywords

Bacterial diseases
Tuberculosis
Mycobacterium tuberculosis
Identification
Genotyping
DNA sequence analysis
Pyrosequencing
Nucleotide sequences
Software
Algorithms
Performance
Signals
Conversion
Laboratory techniques and procedures

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10.1093/bioinformatics/btt339Licence: CC BY-NC

2013bioi1963Final published version, 586 KBLicence: CC BY-NC

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title = "AdvISER-PYRO: amplicon identification using SparsE representation of PYROsequencing signal",

abstract = "Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights <5) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations. Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2\% versus 56.5\%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5\%).",

keywords = "Bacterial diseases, Tuberculosis, Mycobacterium tuberculosis, Identification, Genotyping, DNA sequence analysis, Pyrosequencing, Nucleotide sequences, Software, Algorithms, Performance, Signals, Conversion, Laboratory techniques and procedures",

author = "J. Ambroise and A.S. Piette and C. Delcorps and L. Rigouts and \{de Jong\}, B.C. and L. Irenge and A. Robert and J.L. Gala",

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T1 - AdvISER-PYRO: amplicon identification using SparsE representation of PYROsequencing signal

AU - Ambroise, J.

AU - Piette, A.S.

AU - Delcorps, C.

AU - Rigouts, L.

AU - de Jong, B.C.

AU - Irenge, L.

AU - Robert, A.

AU - Gala, J.L.

N1 - FTX; CC BY NC

PY - 2013

Y1 - 2013

N2 - Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights <5) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations. Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).

AB - Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights <5) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations. Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).

KW - Bacterial diseases

KW - Tuberculosis

KW - Mycobacterium tuberculosis

KW - Identification

KW - Genotyping

KW - DNA sequence analysis

KW - Pyrosequencing

KW - Nucleotide sequences

KW - Software

KW - Algorithms

KW - Performance

KW - Signals

KW - Conversion

KW - Laboratory techniques and procedures

UR - https://www.webofscience.com/wos/woscc/full-record/WOS:000322337400006

U2 - 10.1093/bioinformatics/btt339

DO - 10.1093/bioinformatics/btt339

M3 - A1: Peer-reviewed journal articles

C2 - 23772051

SN - 1367-4803

VL - 29

SP - 1963

EP - 1969

JO - Bioinformatics

JF - Bioinformatics

IS - 16

ER -

AdvISER-PYRO: amplicon identification using SparsE representation of PYROsequencing signal

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Keywords

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