The Experts below are selected from a list of 19287 Experts worldwide ranked by ideXlab platform
David Tse - One of the best experts on this subject based on the ideXlab platform.
-
Optimal assembly for high throughput Shotgun Sequencing.
BMC bioinformatics, 2013Co-Authors: Guy Bresler, Ma'ayan Bresler, David TseAbstract:We present a framework for the design of optimal assembly algorithms for Shotgun Sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earlier works, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes, including the GAGE datasets. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction. The conditions can be viewed as the Shotgun Sequencing analogue of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by Hybridization.
-
Optimal DNA Shotgun Sequencing: Noisy reads are as good as noiseless reads
arXiv: Information Theory, 2013Co-Authors: Abolfazl S. Motahari, Kannan Ramchandran, David TseAbstract:We establish the fundamental limits of DNA Shotgun Sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold which can be surprisingly high. As an example, for a uniformly distributed DNA sequence and a symmetric substitution noisy read channel, the threshold is as high as 19%.
-
Information Theory of DNA Shotgun Sequencing
IEEE Transactions on Information Theory, 2013Co-Authors: Abolfazl S. Motahari, Guy Bresler, David TseAbstract:DNA Sequencing is the basic workhorse of modern day biology and medicine. Shotgun Sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. A basic question is: given a Sequencing technology and the statistics of the DNA sequence, what is the minimum number of reads required for reliable reconstruction? This number provides a fundamental limit to the performance of any assembly algorithm. For a simple statistical model of the DNA sequence and the read process, we show that the answer admits a critical phenomenon in the asymptotic limit of long DNA sequences: if the read length is below a threshold, reconstruction is impossible no matter how many reads are observed, and if the read length is above the threshold, having enough reads to cover the DNA sequence is sufficient to reconstruct. The threshold is computed in terms of the Renyi entropy rate of the DNA sequence. We also study the impact of noise in the read process on the performance.
-
ISIT - Optimal DNA Shotgun Sequencing: Noisy reads are as good as noiseless reads
2013 IEEE International Symposium on Information Theory, 2013Co-Authors: Abolfazl S. Motahari, Kannan Ramchandran, David TseAbstract:We establish the fundamental limits of DNA Shotgun Sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold which can be surprisingly high. As an example, for a uniformly distributed DNA sequence and a symmetric substitution noisy read channel, the threshold is as high as 19%.
-
Information Theory of DNA Shotgun Sequencing
arXiv: Information Theory, 2012Co-Authors: Abolfazl S. Motahari, Guy Bresler, David TseAbstract:DNA Sequencing is the basic workhorse of modern day biology and medicine. Shotgun Sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. A basic question is: given a Sequencing technology and the statistics of the DNA sequence, what is the minimum number of reads required for reliable reconstruction? This number provides a fundamental limit to the performance of {\em any} assembly algorithm. For a simple statistical model of the DNA sequence and the read process, we show that the answer admits a critical phenomena in the asymptotic limit of long DNA sequences: if the read length is below a threshold, reconstruction is impossible no matter how many reads are observed, and if the read length is above the threshold, having enough reads to cover the DNA sequence is sufficient to reconstruct. The threshold is computed in terms of the Renyi entropy rate of the DNA sequence. We also study the impact of noise in the read process on the performance.
Abolfazl S. Motahari - One of the best experts on this subject based on the ideXlab platform.
-
Optimal DNA Shotgun Sequencing: Noisy reads are as good as noiseless reads
arXiv: Information Theory, 2013Co-Authors: Abolfazl S. Motahari, Kannan Ramchandran, David TseAbstract:We establish the fundamental limits of DNA Shotgun Sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold which can be surprisingly high. As an example, for a uniformly distributed DNA sequence and a symmetric substitution noisy read channel, the threshold is as high as 19%.
-
Information Theory of DNA Shotgun Sequencing
IEEE Transactions on Information Theory, 2013Co-Authors: Abolfazl S. Motahari, Guy Bresler, David TseAbstract:DNA Sequencing is the basic workhorse of modern day biology and medicine. Shotgun Sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. A basic question is: given a Sequencing technology and the statistics of the DNA sequence, what is the minimum number of reads required for reliable reconstruction? This number provides a fundamental limit to the performance of any assembly algorithm. For a simple statistical model of the DNA sequence and the read process, we show that the answer admits a critical phenomenon in the asymptotic limit of long DNA sequences: if the read length is below a threshold, reconstruction is impossible no matter how many reads are observed, and if the read length is above the threshold, having enough reads to cover the DNA sequence is sufficient to reconstruct. The threshold is computed in terms of the Renyi entropy rate of the DNA sequence. We also study the impact of noise in the read process on the performance.
-
ISIT - Optimal DNA Shotgun Sequencing: Noisy reads are as good as noiseless reads
2013 IEEE International Symposium on Information Theory, 2013Co-Authors: Abolfazl S. Motahari, Kannan Ramchandran, David TseAbstract:We establish the fundamental limits of DNA Shotgun Sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold which can be surprisingly high. As an example, for a uniformly distributed DNA sequence and a symmetric substitution noisy read channel, the threshold is as high as 19%.
-
Information Theory of DNA Shotgun Sequencing
arXiv: Information Theory, 2012Co-Authors: Abolfazl S. Motahari, Guy Bresler, David TseAbstract:DNA Sequencing is the basic workhorse of modern day biology and medicine. Shotgun Sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. A basic question is: given a Sequencing technology and the statistics of the DNA sequence, what is the minimum number of reads required for reliable reconstruction? This number provides a fundamental limit to the performance of {\em any} assembly algorithm. For a simple statistical model of the DNA sequence and the read process, we show that the answer admits a critical phenomena in the asymptotic limit of long DNA sequences: if the read length is below a threshold, reconstruction is impossible no matter how many reads are observed, and if the read length is above the threshold, having enough reads to cover the DNA sequence is sufficient to reconstruct. The threshold is computed in terms of the Renyi entropy rate of the DNA sequence. We also study the impact of noise in the read process on the performance.
Robin Patel - One of the best experts on this subject based on the ideXlab platform.
-
Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis.
Journal of clinical microbiology, 2020Co-Authors: Matthew Thoendel, Patricio Jeraldo, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Kerryl E. Greenwood-quaintance, Janet Yao, Robin PatelAbstract:Metagenomic Shotgun Sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large complicated data is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic Shotgun Sequencing tools, CosmosID, One Codex, and IDbyDNA were compared to determine whether they result in similar interpretations of the same Sequencing data. We selected 24 diverse samples from a previously characterized data set derived from DNA extracted from biofilms dislodged from the surfaces of resected arthroplasties (sonicate fluid). Sequencing data sets were analyzed using the three commercial tools and compared to culture results and prior metagenomic analysis interpretation. Identical interpretations from all three tools occurred for 6 samples. The total number of species identified included 28 by CosmosID, 59 by One Codex, and 41 by IDbyDNA. All tools performed similarly in detecting those microorganisms identified by culture, including polymicrobial mixes. These data show that while all tools performed well overall, there were some notable differences, particularly in their predilection towards identifying low abundance or contaminant organisms as present.
-
application of metagenomic Shotgun Sequencing to detect vector borne pathogens in clinical blood samples
PLOS ONE, 2019Co-Authors: Prakhar Vijayvargiya, Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwoodquaintance, Nicholas Chia, Zerelda Esquer Garrigos, Rizwan M Sohail, Bobbi S Pritt, Robin PatelAbstract:Background Vector-borne pathogens are a significant public health concern worldwide. Infections with these pathogens, some of which are emerging, are likely under-recognized due to the lack of widely-available laboratory tests. There is an urgent need for further advancement in diagnostic modalities to detect new and known vector-borne pathogens. We evaluated the utility of metagenomic Shotgun Sequencing (MGS) as a pathogen agnostic approach for detecting vector-borne pathogens from human blood samples. Methods Residual whole blood samples from patients with known infection with Babesia microti, Borrelia hermsii, Plasmodium falciparum, Mansonella perstans, Anaplasma phagocytophilum or Ehrlichia chaffeensis were studied. Samples underwent DNA extraction, removal of human DNA, whole genome amplification, and paired-end library preparation, followed by Sequencing on Illumina HiSeq 2500. Bioinformatic analysis was performed using the Livermore Metagenomics Analysis Toolkit (LMAT), Metagenomic Phylogenetic Analysis (MetaPhlAn2), Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) and Kraken 2. Results Eight samples were included in the study (2 samples each for P. falciparum and A. phagocytophilum). An average of 27.5 million read pairs was generated per sample (range, 18.3–38.8 million) prior to removal of human reads. At least one of the analytic tools was able to detect four of six organisms at the genus level, and the organism present in five of eight specimens at the species level. Mansonella and Ehrlichia species were not detected by any of the tools; however, mitochondrial cytochrome c oxidase subunit I amino acid sequence analysis suggested the presence of M. perstans genetic material. Conclusions MGS is a promising tool with the potential to evolve as a non-hypothesis driven diagnostic test to detect vector-borne pathogens, including protozoa and helminths.
-
direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic Shotgun Sequencing
Journal of Clinical Microbiology, 2018Co-Authors: Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwoodquaintance, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Aaron J Tande, Jayawant N Mandrekar, Robin PatelAbstract:Metagenomic Shotgun Sequencing has the potential to transform how serious infections are diagnosed by offering universal, culture-free pathogen detection. This may be especially advantageous for microbial diagnosis of prosthetic joint infection (PJI) by synovial fluid analysis since synovial fluid cultures are not universally positive and since synovial fluid is easily obtained preoperatively. We applied a metagenomics-based approach to synovial fluid in an attempt to detect microorganisms in 168 failed total knee arthroplasties. Genus- and species-level analyses of metagenomic Sequencing yielded the known pathogen in 74 (90%) and 68 (83%) of the 82 culture-positive PJIs analyzed, respectively, with testing of two (2%) and three (4%) samples, respectively, yielding additional pathogens not detected by culture. For the 25 culture-negative PJIs tested, genus- and species-level analyses yielded 19 (76%) and 21 (84%) samples with insignificant findings, respectively, and 6 (24%) and 4 (16%) with potential pathogens detected, respectively. Genus- and species-level analyses of the 60 culture-negative aseptic failure cases yielded 53 (88%) and 56 (93%) cases with insignificant findings and 7 (12%) and 4 (7%) with potential clinically significant organisms detected, respectively. There was one case of aseptic failure with synovial fluid culture growth; metagenomic analysis showed insignificant findings, suggesting possible synovial fluid culture contamination. Metagenomic Shotgun Sequencing can detect pathogens involved in PJI when applied to synovial fluid and may be particularly useful for culture-negative cases.
-
A Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2017Co-Authors: Matthew Thoendel, Patricio Jeraldo, Matthew P Abdel, Nicholas Chia, Kerryl E. Greenwood-quaintance, James M. Steckelberg, Douglas R. Osmon, Robin PatelAbstract:Defining the microbial etiology of culture-negative prosthetic joint infection (PJI) can be challenging. Metagenomic Shotgun Sequencing is a new tool to identify organisms undetected by conventional methods. We present a case where metagenomics was used to identify Mycoplasma salivarium as a novel PJI pathogen in a patient with hypogammaglobulinemia.
-
Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis.
Journal of clinical microbiology, 2017Co-Authors: Matthew Thoendel, Patricio Jeraldo, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Kerryl E. Greenwood-quaintance, Janet Yao, Robin PatelAbstract:ABSTRACT Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic Shotgun Sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits can be problematic. Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples. Variations in the number of background reads, the genera identified in the background, and the number of reads from known pathogens known to be present in the samples were observed between kits. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. This approach also resulted in the presence of contaminant bacterial DNA and yielded fewer reads from the known pathogens. These findings highlight the impact that WGA kit selection can have on metagenomic analysis of low-biomass samples and the importance of the careful selection and consideration of the implications of using these tools.
Matthew Thoendel - One of the best experts on this subject based on the ideXlab platform.
-
Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis.
Journal of clinical microbiology, 2020Co-Authors: Matthew Thoendel, Patricio Jeraldo, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Kerryl E. Greenwood-quaintance, Janet Yao, Robin PatelAbstract:Metagenomic Shotgun Sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large complicated data is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic Shotgun Sequencing tools, CosmosID, One Codex, and IDbyDNA were compared to determine whether they result in similar interpretations of the same Sequencing data. We selected 24 diverse samples from a previously characterized data set derived from DNA extracted from biofilms dislodged from the surfaces of resected arthroplasties (sonicate fluid). Sequencing data sets were analyzed using the three commercial tools and compared to culture results and prior metagenomic analysis interpretation. Identical interpretations from all three tools occurred for 6 samples. The total number of species identified included 28 by CosmosID, 59 by One Codex, and 41 by IDbyDNA. All tools performed similarly in detecting those microorganisms identified by culture, including polymicrobial mixes. These data show that while all tools performed well overall, there were some notable differences, particularly in their predilection towards identifying low abundance or contaminant organisms as present.
-
application of metagenomic Shotgun Sequencing to detect vector borne pathogens in clinical blood samples
PLOS ONE, 2019Co-Authors: Prakhar Vijayvargiya, Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwoodquaintance, Nicholas Chia, Zerelda Esquer Garrigos, Rizwan M Sohail, Bobbi S Pritt, Robin PatelAbstract:Background Vector-borne pathogens are a significant public health concern worldwide. Infections with these pathogens, some of which are emerging, are likely under-recognized due to the lack of widely-available laboratory tests. There is an urgent need for further advancement in diagnostic modalities to detect new and known vector-borne pathogens. We evaluated the utility of metagenomic Shotgun Sequencing (MGS) as a pathogen agnostic approach for detecting vector-borne pathogens from human blood samples. Methods Residual whole blood samples from patients with known infection with Babesia microti, Borrelia hermsii, Plasmodium falciparum, Mansonella perstans, Anaplasma phagocytophilum or Ehrlichia chaffeensis were studied. Samples underwent DNA extraction, removal of human DNA, whole genome amplification, and paired-end library preparation, followed by Sequencing on Illumina HiSeq 2500. Bioinformatic analysis was performed using the Livermore Metagenomics Analysis Toolkit (LMAT), Metagenomic Phylogenetic Analysis (MetaPhlAn2), Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) and Kraken 2. Results Eight samples were included in the study (2 samples each for P. falciparum and A. phagocytophilum). An average of 27.5 million read pairs was generated per sample (range, 18.3–38.8 million) prior to removal of human reads. At least one of the analytic tools was able to detect four of six organisms at the genus level, and the organism present in five of eight specimens at the species level. Mansonella and Ehrlichia species were not detected by any of the tools; however, mitochondrial cytochrome c oxidase subunit I amino acid sequence analysis suggested the presence of M. perstans genetic material. Conclusions MGS is a promising tool with the potential to evolve as a non-hypothesis driven diagnostic test to detect vector-borne pathogens, including protozoa and helminths.
-
direct detection and identification of prosthetic joint infection pathogens in synovial fluid by metagenomic Shotgun Sequencing
Journal of Clinical Microbiology, 2018Co-Authors: Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwoodquaintance, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Aaron J Tande, Jayawant N Mandrekar, Robin PatelAbstract:Metagenomic Shotgun Sequencing has the potential to transform how serious infections are diagnosed by offering universal, culture-free pathogen detection. This may be especially advantageous for microbial diagnosis of prosthetic joint infection (PJI) by synovial fluid analysis since synovial fluid cultures are not universally positive and since synovial fluid is easily obtained preoperatively. We applied a metagenomics-based approach to synovial fluid in an attempt to detect microorganisms in 168 failed total knee arthroplasties. Genus- and species-level analyses of metagenomic Sequencing yielded the known pathogen in 74 (90%) and 68 (83%) of the 82 culture-positive PJIs analyzed, respectively, with testing of two (2%) and three (4%) samples, respectively, yielding additional pathogens not detected by culture. For the 25 culture-negative PJIs tested, genus- and species-level analyses yielded 19 (76%) and 21 (84%) samples with insignificant findings, respectively, and 6 (24%) and 4 (16%) with potential pathogens detected, respectively. Genus- and species-level analyses of the 60 culture-negative aseptic failure cases yielded 53 (88%) and 56 (93%) cases with insignificant findings and 7 (12%) and 4 (7%) with potential clinically significant organisms detected, respectively. There was one case of aseptic failure with synovial fluid culture growth; metagenomic analysis showed insignificant findings, suggesting possible synovial fluid culture contamination. Metagenomic Shotgun Sequencing can detect pathogens involved in PJI when applied to synovial fluid and may be particularly useful for culture-negative cases.
-
Direct Detection and Identification of Prosthetic Joint Pathogens in Synovial Fluid (SF) by Metagenomic Shotgun Sequencing
Open Forum Infectious Diseases, 2017Co-Authors: Morgan Ivy, Matthew Thoendel, Patricio Jeraldo, Arlen D Hanssen, Matthew P Abdel, Nicholas Chia, Aaron J Tande, Kerryl E. Greenwood-quaintance, Janet Yao, Jayawant N MandrekarAbstract:Abstract Background Detection and identification of microorganism(s) involved in periprosthetic joint infection (PJI) can inform surgical management and directed antibiotic therapy. Metagenomic Shotgun Sequencing is a powerful tool with the potential to change how many PJIs are diagnosed as it allows direct detection and identification of pathogens in clinical specimens. In the largest series to date, we utilized a metagenomics-based approach applied to SF to define potential microbial etiologies of failed total knee arthroplasties (TKAs). Methods Synovial fluid was collected from 112 failed TKAs [74 PJI and 38 aseptic implant failure (AF)] via preoperative arthrocentesis. Cell count and differential, standardized culture and DNA-based metagenomic Shotgun Sequencing were performed. Human DNA was depleted using the MolYsis basic kit prior to DNA extraction, whole genome amplification, and Sequencing. Taxonomic assignment of reads and pathogen identification was achieved using a pipeline incorporating k-mer- and marker gene-based classification software. A scheme for analysis and filtration of false-positives was created and applied, incorporating cut-offs for the number of reads, quality scores, and coverage across a reference genome. Patients were classified as having PJI using the IDSA criteria and expert review. Analyses were recorded as percent agreement, with 95% confidence intervals (CI), of metagenomics to SF culture. Results Metagenomic analysis identified the known pathogen in 54 (90%) (CI, 79.5%–96.2%) of the 60 culture-positive PJIs analyzed and one (2%) (CI, 0.0%–8.9%) potential polymicrobial infection not detected by culture. For the 14 culture-negative PJIs tested, metagenomics showed 79% (CI, 49.2%–95.3%) agreement for negative findings; potential pathogens were identified in three (21%) (CI, 4.7%–50.8%) culture-negative PJI cases, with one being polymicrobial. Of the 37 culture-negative AF cases, metagenomics showed 97% (CI, 85.8%–99.9%) agreement with negative culture and identified one (3%) (CI, 0.0%–14.2%) potential pathogen. For the one culture-positive AF case, metagenomic results were negative, suggesting possible culture contamination. Conclusion Metagenomic Shotgun Sequencing performed on SF can be used to diagnose PJI and may be particularly useful for culture-negative PJI. Disclosures R. Patel, ASM: Board Member, None; CD Diagnostics, BioFire, Curetis, Merck, Hutchison Biofilm Medical Solutions, Accelerate Diagnostics, Allergan, and The Medicines Company: Grant Investigator, Grant recipient; Curetis: Consultant, Monies paid to my employer; A patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued: Patents, Patents, any money is paid to my employer; Actelion: DSMB, Money paid to my employer; ASM and IDSA: Editor’s stipends, Editor’s stipends; NBME, Up-to-Date and the Infectious Diseases Board Review Course: NBME, Up-to-Date and the Infectious Diseases Board Review Course, Honoraria; Roche, ASM, and IDSA: Travel reimbursement, Travel reimbursement
-
A Novel Prosthetic Joint Infection Pathogen, Mycoplasma salivarium, Identified by Metagenomic Shotgun Sequencing.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2017Co-Authors: Matthew Thoendel, Patricio Jeraldo, Matthew P Abdel, Nicholas Chia, Kerryl E. Greenwood-quaintance, James M. Steckelberg, Douglas R. Osmon, Robin PatelAbstract:Defining the microbial etiology of culture-negative prosthetic joint infection (PJI) can be challenging. Metagenomic Shotgun Sequencing is a new tool to identify organisms undetected by conventional methods. We present a case where metagenomics was used to identify Mycoplasma salivarium as a novel PJI pathogen in a patient with hypogammaglobulinemia.
Jeong-hyeon Choi - One of the best experts on this subject based on the ideXlab platform.
-
ESTclean: a cleaning tool for next-gen transcriptome Shotgun Sequencing
BMC bioinformatics, 2012Co-Authors: Hongseok Tae, Dong-sung Ryu, Suhas Sureshchandra, Jeong-hyeon ChoiAbstract:Background With the advent of next-generation Sequencing (NGS) technologies, full cDNA Shotgun Sequencing has become a major approach in the study of transcriptomes, and several different protocols in 454 Sequencing have been invented. As each protocol uses its own short DNA tags or adapters attached to the ends of cDNA fragments for labeling or Sequencing, different contaminants may lead to mis-assembly and inaccurate sequence products.
