Amplicon sequencing. Medical search. Frequent questions

MiSeq amplicon high-throughput sequencing (Illumina ® ) is able to detect species richness (the number of species within a community) and species evenness (the sizes of species populations within a community). (degruyter.com)
Also known as targeted sequencing, this set of technologies allows high-throughput, high multiplexing, targeted loci sequencing on Illumina NGS platforms. (cornell.edu)
Open access software, iVar , to generate consensus sequences and identify intrahost variants from Illumina amplicon data. (grubaughlab.com)
The Illumina protocols, iVar, and many of the amplicon sets were developed by Kristian Andersen, Karthik Gangavaru, and Glenn Oliveira. (grubaughlab.com)
2 Lighten J, van Oosterhout C, Paterson IG, McMullan M, Bentzen P. Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata). (edu.pl)
The ESPSF currently supports the Illumina NextSeq 2000 and Illumina MiSeq for high-throughput sequencing. (anl.gov)
Applications on both the Illumina NextSeq 2000 and MiSeq include shotgun metagenome sequencing, metatranscriptome sequencing, rRNA-based amplicon library sequencing, and genome sequencing and resequencing. (anl.gov)
You can upload directly the data out of the sequencing machines (Illumina, etc). (who.int)
Sequencing was conducted by tiled amplicon PCR using ARTIC v1 or v3 primers and Illumina sequencing. (who.int)

This research is the first non-culture-based study to analyse the similarities and dissimilarities of the faecal microbiome by using 16S amplicon based metagenomics coupled with NGS (next generation sequencing) in different Swedish breeds of sheep and goat (outgroup). (slu.se)
Eine besondere Anwendung von Amplicon Sequenzierungen ist das 16S Sequencing zur Bestimmung mikrobieller Spezies aus natürlichen Populationen (Mikrobiom Metagenomics). (hhu.de)
Expansion of high-throughput sequencing (HTS) technologies and reduction in analysis costs has allowed for detailed exploration of various habitats with use of amplicon, metagenomics, and metatranscriptomics approaches. (gla.ac.uk)

For MiSeq most publications present results of V4 sequencing (e.g. (seqanswers.com)
So, what are the advantages/disadvantages to use V1-2 or V4 of the 16S to sequence on MiSeq? (seqanswers.com)
Sequencing libraries of these amplicons were made and the libraries read on a MiSeq instrument. (opensourcebiology.eu)
The MiSeq run was single-end and so I want to look for the forward primer sequence in the resultant fastq files. (opensourcebiology.eu)

AmpliLEGACY emulates previously published methods for genotyping amplicon sequencing data. (edu.pl)

ASVs are also referred to as exact sequence variants (ESVs), zero-radius OTUs (ZOTUs), sub-OTUs (sOTUs), haplotypes, or oligotypes. (wikipedia.org)
The total of (10734) amplicon sequence variants (ASV) after the filtration were employed for the phylogeny and taxonomy analysis of bacteria at the phylum and genus level. (slu.se)
Diatom composition data, in the form of amplicon sequencing variants, were obtained via high throughput sequencing of filtered biomass samples. (bco-dmo.org)
Sequencing data were analyzed with QIIME2 and taxonomic identification was performed using the q2-feature-classifier QIIME2 plugin, the Greengenes Database, and amplicon sequence variants (ASV) analysis. (frontiersin.org)
Methods: Ninety-seven urothelial (61 upper tract and 28 bladder) tumors diagnosed from 1980 to 2017 in carriers of Lynch syndrome-associated pathogenic MMR variants and their first-degree relatives (FDR) were analyzed by MMR protein immunohistochemistry, the MSI Analysis System v1.2 (Promega), and an amplicon sequencing-based MSI assay. (lu.se)

Before that, for many years the standard unit for marker-gene analysis was the operational taxonomic unit (OTU), which is generated by clustering sequences based on a threshold of similarity. (wikipedia.org)
Assigning amplicon sequences to operational taxonomic units (OTUs) is an important step in characterizing microbial communities across large data sets. (nih.gov)
Efficient and robust software tools are needed to assign microbial sequences into taxonomic groups for characterization and comparison of communities. (nih.gov)
The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. (pensoft.net)
Some unidentified sequences were also present at each taxonomic level. (pensoft.net)
Targeted sequencing of a phylogenetic marker gene allows us to profile the taxonomic composition of a specific microbial kingdom, such as bacteria or fungi. (biomcare.com)
Recent amplicon sequence variant (ASV)-based analyses of 16S rRNA genes differ from that based on operational taxonomic unit (OTU) clustering in the way it deals with sequences having potential errors. (preprints.org)
Taxonomic assignment, using the naïve Bayes classifier trained with the V3-V4 region of reference 16S rRNA sequences in the extended human oral microbiome database (eHOMD), resulted in bacterial compositions similar to those of OTU-based analyses. (preprints.org)
Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)

AmpSeq and rhAmpSeq use a large set of primers with known sequences to create amplicons throughout the genome. (cornell.edu)
These loci are initially amplified by a first PCR with tailed, locus-specific primers, then barcoded by a second PCR with indexed primers for sequencing. (cornell.edu)
Ultra-degenerate primers with 3' termini overlapping the probe-binding site adapt the target through site-directed mutagenesis during qPCR to replace DRM-proximal sequence variation. (nature.com)
Unlike a typical PCR experiment with a single set of forward and reverse primers, amplicon sequencing panels include multiple sets of primer pairs to copy multiple regions of the DNA simultaneously. (idtdna.com)

Amplicon metagenomic sequencing 16S, ITS. (biomcare.com)

We used deep sequencing of the 16S rRNA gene from transfusion, France. (cdc.gov)
In our amplicon sequencing services, we profile the bacterial microbiome by sequencing the 16S rRNA gene, and we profile the fungi microbiome by sequencing the internal transcribed spacer 2 (ITS2) sequence (the mycobiome). (biomcare.com)
Please see below for some more information about the 16S rRNA gene and the ITS sequence. (biomcare.com)
It also does not attempt to normalize each amplicon at the gene level, though this may be addressed in a future version of CNVkit. (readthedocs.io)
To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea . (springer.com)
Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. (edu.sa)
Evaluation of nanopore-based sequencing technology for gene marker based analysis of complex microbial communities. (gla.ac.uk)
All sequences were compared by alignment with the pure culture and a C. beticola actin gene sequence from GenBank. (usda.gov)
All sequences as well as C. beticola from amended field soil and pure culture were compared by alignment with a C. beticola actin gene sequence from GenBank. (usda.gov)
The full HA and NA genes of 16 H1N1-positive samples obtained in our study and 21 published HA sequences and 20 published NA sequences from Jordanian viruses that were available on online gene databases were analysed. (who.int)
The laboratory procedure is based on amplifying and sequencing four variable regions of the 16S rRNA gene with two amplicons. (folkhalsomyndigheten.se)

Because these analyses, also called "amplicon reads," are created following the removal of erroneous sequences generated during PCR and sequencing, using ASVs makes it possible to distinguish sequence variation by a single nucleotide change. (wikipedia.org)
IMPORTANCE Advancements in DNA sequencing technology have allowed researchers to affordably generate millions of sequence reads from microorganisms in diverse environments. (nih.gov)
Maximum number of amplicon sequences/reads to be processed. (edu.pl)
Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. (pensoft.net)
CNVkit is designed for use on hybrid capture sequencing data, where off-target reads are present and can be used improve copy number estimates. (readthedocs.io)
As Pat said, and Rob Knight would agree, the V4 region is good because you can get nearly full overlap of the two reads, which should reduce sequencing noise in your data and thus help prevent OTU inflation. (seqanswers.com)
We investigated the optimal parameters for sequence denoising, using DADA2, and found the trimming of the first 20 nucleotides from 5′-end of both paired reads avoided excessive sequence loss during chimera removal. (preprints.org)
Truncating reads at positions 240-245 allowed the removal of low-quality sequences while maintaining sufficient length to merge matching paired ends. (preprints.org)
However, the abundance of long ITDs (≥75nt) was underestimated by HTAS, as the size of the ITD affected the mappability of the corresponding sequence reads. (oncotarget.com)

The procedure's high sequence depth allows for these amplicons to be analysed separetely so different bacteria from the same sample can be identified. (folkhalsomyndigheten.se)

This method uses PCR to create copies of your targeted DNA sequences to create amplicons. (idtdna.com)

Dadurch können über Multiplexing Protokolle viele Proben auf einmal bearbeitet werden, wodurch die Kosten deutlich geringer sind als bei Whole Genome Sequencing Protokollen. (hhu.de)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)
Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)
Methods of ctDNA analysis include single-locus assays, targeted sequencing approaches, and whole genome sequencing. (medscape.com)
Whole genome sequencing, particularly low-coverage whole genome sequencing, is also being very effectively used these days to characterize copy number changes," said Dawson. (medscape.com)

Assessment of two-pool multiplex long-amplicon nanopore sequencing of SARS-CoV-2. (bvsalud.org)
Here we developed a two-pool, long-amplicon 36-plex PCR primer panel with ~1000-bp amplicon lengths for full- genome sequencing of SARS-CoV-2 . (bvsalud.org)
Therefore, PacBio® long amplicon sequencing was evaluated for mutant characterization in alfalfa. (usda.gov)

We estimated that ~5 Mbp nanopore sequencing data may ensure a >95% viral genome coverage with a ≥10-fold depth and may generate reliable genomes at consensus sequence levels. (bvsalud.org)
The focus of this study is on the evaluation of nanopore sequencing data: read quality, sequencing errors, alignment quality but also bacterial community structure. (gla.ac.uk)

Amplicon sequencing is a cost-effective approach for profiling a specific part of the microbiome and can be used for most any sample - including soil, water, skin, and stool - to detect the different species found in the sample. (biomcare.com)
It has some advantages over shotgun sequencing for samples with low microbiome concentration. (biomcare.com)

The uses of ASVs include classifying groups of species based on DNA sequences, finding biological and environmental variation, and determining ecological patterns. (wikipedia.org)
Therefore, ASVs represent a finer distinction between sequences. (wikipedia.org)
For these researchers, the utility of finer sequence resolution (precision) and the advantage of being able to easily compare sequences between different studies (tractability and reproducibility) make ASVs the better option for analyzing sequence differences. (wikipedia.org)

However, one may wish to incorporate new samples to previously clustered data sets without clustering all sequences again, such as when comparing across data sets or deploying machine learning models. (nih.gov)
The OptiClust algorithm produces high-quality groups by comparing sequences to each other, but the assignments can change when new sequences are added to a data set, making it difficult to compare different studies. (nih.gov)
Open access methods to process and generate consensus sequences from MinION amplicon data. (grubaughlab.com)
Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequencing Facility are intended for research purposes only. (wisc.edu)
The amplicons from different research samples can be pooled (referred to as multiplexing) which involves adding a barcode or index sequence to the samples so they can be identified during data analysis. (idtdna.com)
For projects where you have purchased both sequencing and data analysis, we deliver three reports with descriptions of the data, the processing, analysis, and the results of the statistical analysis, together with illustrations and tables. (biomcare.com)
By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. (osti.gov)
The raw sequencing data was processed using the SMRT link platform and analyzed using a workflow on the Geneious® software. (usda.gov)
Furthermore, this study developed sophisticated library preparation and data analyses methods to enable high-accuracy analysis of amplicon libraries from complex microbial communities for sequencing on the nanopore platform. (gla.ac.uk)
Data from this study alongside previous studies, suggest that universal MMR deficiency testing of newly diagnosed urothelial cancers, using immunohistochemistry and/or sequencing-based MSI analysis of sensitive markers, offer a potentially useful approach to identification of Lynch syndrome cases. (lu.se)
This hands on course will give you the experience and provide the tools that are needed to analyze next generation sequencing data. (lu.se)
Flomics Biotech is developing a cloud-based server that enables automated data analysis of Next Generation Sequencing SARS-CoV-2 data. (who.int)
or amplicon-based sequencing data. (who.int)
All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)
The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)

You can view Archer assays alongside IDT's xGen™ NGS portfolio to find the best next generation sequencing solution for your lab. (idtdna.com)
The deployment of multiplex PCR assays that target SARS-CoV-2 followed by either massively parallel or nanopore sequencing is a widely-used strategy to obtain genome sequences from primary samples. (bvsalud.org)
Plants recovered from tissue culture were first screened for targeted mutations using combinations of the cleaved amplified polymorphic sequences (CAPS) or the target amplicon clone and sequencing assays (TACAS). (usda.gov)
Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
Of the 11 tumors with retained MMR protein expression, four were MSI-low/MSI-high or MSI-high by the Promega assay or one of the sequencing-based assays. (lu.se)

The difference with AmpSeq or rhAmpSeq is that rAmpSeq does not amplify known sequences, but ALL the sequences in the genome that are flanking a known sequence. (cornell.edu)

Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions. (idtdna.com)
Amplicon sequencing is an experimental method of targeted next generation sequencing (NGS) that enables you to research the sequence of specific genomic regions. (idtdna.com)
MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout. (edu.pl)
The ESPSF was originally established in 2007 at Argonne National Laboratory and is housed in Argonne's Computing, Environment and Life Sciences ( CELS ) directorate, providing world-class computation power, software, and expertise critical to the acquisition, analysis, and interpretation of the unprecedented volume of genetic information being generated on next generation DNA sequencing platforms. (anl.gov)
Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales. (edu.sa)
NBL also uses next-generation sequencing methods to characterize and subtype Clostridium botulinum and related organisms, including a national molecular surveillance database for comparing genetic relatedness among strains across the United States and identifying trends among botulism cases. (cdc.gov)
Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections. (who.int)
The Public Health Agency's Next Generation Sequencing (NGS) platform performs massive parallel sequencing of DNA and RNA. (folkhalsomyndigheten.se)
Polymerase chain reaction is a technique commonly used for interrogating the presence or absence of a particular mutation, and next-generation sequencing techniques can include targeted sequencing approaches. (medscape.com)

In addition, the protocol details a procedure to screen mutant plants fast and effectively using Pacbio amplicon sequencing. (usda.gov)

Originally developed for Zika virus, our simple and scalable amplicon-based sequencing approach, PrimalSeq , can be used for a variety of viruses. (grubaughlab.com)
Try the amplicon-based PrimalSeq approach adapted for use on the hand-held MinION. (grubaughlab.com)
Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.2. (protocols.io)

An amplicon sequence variant (ASV) is any one of the inferred single DNA sequences recovered from a high-throughput analysis of marker genes. (wikipedia.org)
ESPSF is involved in a wide range of scientific research from the sequencing of metagenomic samples to both 16S and 18S rRNA amplicon sequencing for microbial community analysis, and ITS sequencing for fungal community analysis. (anl.gov)
Analysis of these sequences seems to suggest that at least some of the herbarium specimens may be inaccurately identified-potentially harboring undescribed species. (dannyhaelewaters.com)
At diagnosis, the FLT3- ITD status is routinely assessed by fragment analysis, providing information about the length but not the position and sequence of the ITD. (oncotarget.com)
This research project investigated the potential of a novel nanopore-based sequencing platform from Oxford Nanopore Technologies (ONT) for rapid and accurate analysis of various environmentally complex samples. (gla.ac.uk)
This work opens a new possibility for accurate, in-field amplicon analysis of complex samples with the use of MinIONTM and for the development of autonomous biosensing technology for culture-free detection of pathogenic and non-pathogenic microorganisms in water, soil, food, drinks or blood. (gla.ac.uk)
Two sets of MSI markers were used in sequencing-based MSI analysis: a panel of 24 and 54 markers developed for colorectal cancer and blood MSI analysis, respectively. (lu.se)
The Promega MSI assay was significantly less sensitive, but the 54-marker sequencing-based MSI analysis showed no significant difference compared to immunohistochemistry. (lu.se)
HA and NA sequences each in the analysis. (who.int)
Consensus sequences were generated, sequences were aligned to a reference sequence, and phylogenetic analysis performed. (who.int)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)

In situations where there are expected to be relatively few microorganisms in the samples, amplicon sequencing has an advantage over shotgun sequencing as it targets the organism of interest and therefore does not use a lot of reagent to sequence other types of DNA in the sample. (biomcare.com)
It is cheaper than shotgun sequencing although the cost difference continues to reduce, and mostly depends on the desired sequencing depth and the sample type. (biomcare.com)

NARST accomplishes these goals for surveillance on sporadic cases, outbreaks of illness, and special studies by conducting susceptibility testing and sequencing whole pathogen genomes. (cdc.gov)
Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. (folkhalsomyndigheten.se)

Putative erroneous sequences with same or higher frequency respect to the parental variant will be assumed to be true alleles. (edu.pl)

Barcoded amplicon sequencing technique was used to study the microbial communities. (pensoft.net)
Nucleic acid sequencing can provide a detailed overview of microbial communities in comparison with standard plate-culture methods. (gla.ac.uk)

Individual research samples used for amplicon sequencing must be transformed into libraries by adding adapters and enriching target regions to each of the amplicons with a second PCR amplification or adapter ligation. (idtdna.com)
However, this approach does not collect any copy number information between targeted regions, so it should only be used if you have in fact prepared your samples with a targeted amplicon sequencing protocol. (readthedocs.io)
I plan to sequence fish fin samples to investigate mucosal microbiota. (seqanswers.com)
The bacterial composition of oral samples has traditionally been determined by PCR amplicon sequencing of 16S rRNA genes. (preprints.org)
For this reason, mock bacterial community samples were generated, sequenced and analysed with use of multiple bioinformatics approaches. (gla.ac.uk)
Seventy-two samples had sufficient DNA for the sequencing-based MSI assay, of which 55 (76.4%) and 61 (84.7%) scored as MSI-high using the 24-marker and 54-marker panels, respectively. (lu.se)
[ 5 ] The researchers characterized genomic architecture and inferred the clonal evolution using eight tumor biopsies and nine plasma samples collected over 1193 days of clinical follow-up using exome and targeted amplicon sequencing. (medscape.com)
Mutation levels in the plasma samples reflected the clonal hierarchy inferred from sequencing of tumor biopsies. (medscape.com)

ASV methods on the other hand are able to resolve sequence differences by as little as a single nucleotide change, thus avoiding similarity-based operational clustering units altogether. (wikipedia.org)

Sequencing-based approaches for patho- sequencing in cerebrospinal fluid. (cdc.gov)
Other approaches assign sequences to groups by comparing them to sequences in a reference database to produce consistent assignments, but the quality of the groups produced is reduced compared to that with OptiClust. (nih.gov)
These approaches are useful if you want cost-effective sequencing at a specific set of loci in the genome. (cornell.edu)

reverse transcription PCR cycle threshold value and found that ≥90% of viral genomes could be covered with high sequencing depths (≥20% mean depth). (bvsalud.org)

These methods work broadly by generating an error model tailored to an individual sequencing run and employing algorithms that use the model to distinguish between true biological sequences and those generated by error. (wikipedia.org)
A notable difference between de novo clustering and database-dependent reference clustering methods is that OTU assignments from de novo methods may change when new sequences are added. (nih.gov)
Existing reference-based methods produce consistent OTUs but only consider the similarity of each query sequence to a single reference sequence in an OTU, resulting in assignments that are worse than those generated by de novo methods. (nih.gov)
By default, sequencing methods provide information about the relative abundance of microorganisms in a sample. (biomcare.com)
My research group focus on enabling high-throughput investigation of uncultivated microbes in complex environments using DNA sequencing by developing new methods that increase throughput at least 10-fold. (aau.dk)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)

I used nearly 90 primer pairs to multiplex a PCR reaction to generate amplicons. (opensourcebiology.eu)

Fariq A, Yasmin A, Blazier JC, Jannat S (2021) Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing. (pensoft.net)
16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)
The method uses an internal control sequence (spike) which is amplified and sequenced simultaneously with the sample to facilitate the assessment of the bacterial content and to detect amplification-inhibiting factors in the sample that may lead to a negative result. (folkhalsomyndigheten.se)

Only sequences that satisfy theoretical marker lengths can be 'dominant' within a cluster. (edu.pl)
These are the two marker regions most often purchased via our amplicon sequencing service. (biomcare.com)

In recent years the ESPSF has also established expertise sequencing pathogens from wastewater. (anl.gov)
In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)

Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (who.int)

Shortening primer sequences to 7-9 nts can increase the number of retrieved sequences (eg. (edu.pl)
I have 4 fastq files to query these primer sequences. (opensourcebiology.eu)

Explain how the final grade will be calculated (variant calling, amplicon sequencing, project, exam). (lu.se)

HaloPlex HS is a high-sensitivity, amplicon-based targeted sequencing method that incorporates molecular barcodes in the DNA library. (agilent.com)
Lee, S., Yamamoto, N. (2015) Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus . (degruyter.com)
qPCR probe design is more averse to similar modifications because increasing probe T m through nucleotide degeneracy or sequence lengthening may lead to high T m variations that reduce specific target discrimination. (nature.com)
A study reported the microbial diversity of three hot springs from Neuquén, Argentina, by using molecular based high-throughput amplicon sequencing technique. (pensoft.net)
The Environmental Sample Preparation and Sequencing Facility at Argonne National Laboratory is a state-of-the-art facility for nucleic acid extraction, library preparation, and ultra-high throughput sequencing. (anl.gov)
To overcome this limitation, we performed cDNA-based high-throughput amplicon sequencing (HTAS) in 250 FLT3- ITD positive AML patients, treated on German AML Cooperative Group (AMLCG) trials. (oncotarget.com)
The sequences were are associated with high morbidity and submitted to GenBank under accession mortality ( 1 ). (who.int)

The goal of this project is to revise species names of the sequenced herbarium collections of Lactifluus . (dannyhaelewaters.com)

Although OTUs do not provide such precise and accurate measurements of sequence variation, they are still an acceptable and valuable approach. (wikipedia.org)
To provide an efficient method to fit sequences to existing OTUs, we developed the OptiFit algorithm. (nih.gov)
Inspired by the de novo OptiClust algorithm, OptiFit considers the similarity of all pairs of reference and query sequences to produce OTUs of the best possible quality. (nih.gov)

We found the platform to be rapid and accurate at characterizing multiple targets across all four haplo-alleles in single sequencing run. (usda.gov)

However, multiplex PCR -based sequencing carries an inherent bias of sequencing depth among different amplicons, which may cause uneven coverage. (bvsalud.org)

Sequences will be added to a curated dataset of Lactifluus to help with identification. (dannyhaelewaters.com)

This library prep type enables identification of thousands of polymorphisms in the low copy intervening sequences of repetitive elements. (cornell.edu)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

Is there a way to query the sequences in primer file with fastq file and get the counts for each primer name in a new output file. (opensourcebiology.eu)

Agilent׷ HaloPlex / HaloPlex HS amplicon-based technology for target enrichment and amplification offers an NGS solution with speed, accuracy, and sensitivity. (agilent.com)
We add adaptors on amplicons you already made during the first PCR amplification. (cornell.edu)
We systematically violated canonical qPCR design principles to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a point mutation assay that mitigates the impact of sequence variation on probe-based qPCR performance. (nature.com)
The adapters can either include the index sequences or can be added during the PCR amplification step. (idtdna.com)

The PCR fragment size of C. beticola from the amended field soil correlated in size with the amplicon from control C. beticola culture DNA extract. (usda.gov)

It also made recommendations for the complete genome sequencing of all currently retained isolates in both repositories. (who.int)

Total DNA of naso-oropharyngeal swabs from 74 women with or without breast cancer, positive or negative for SARS-CoV-2 were PCR-amplified for 16S-rDNA V3 and V4 regions and submitted to massive parallel sequencing. (frontiersin.org)

Depending upon the number of amplicons in the targeted sequencing library, one lane of the sequencing flow cell can decode hundreds to thousands of indexed libraries. (idtdna.com)
As seen in Figure 1, xGen NGS Amplicon Sequencing technology uses multiple overlapping amplicons in a single tube, using a rapid, 2-hour workflow to prepare ready-to-sequence libraries for research studies. (idtdna.com)

Modern metagenomic studies, like 16S rRNA sequencing, accurately characterise microbial diversity. (pensoft.net)

A previous study sequenced Lactifluus specimens from the Herbarium Universitatis Gandavensis. (dannyhaelewaters.com)
This work resulted in good-quality ITS and RPB2 sequences for some 60 specimens. (dannyhaelewaters.com)
Finally, there will be the option the link specimens with miombo woodland soil sequences-to further our understanding of the ecology and host associations of these understudied fungi. (dannyhaelewaters.com)

Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea . (springer.com)

4 such reactions, differing in some primer pairs were used for sequencing. (opensourcebiology.eu)

If your research requires rapid, ready-to-sequence materials or you are working with low-input quantities, xGen NGS can unlock the answers you seek. (idtdna.com)

Sequencing viruses in the field? (grubaughlab.com)

16S/18S/ITS Amplicon Metagenomic Sequencing is an ultra-deep DNA sequencing method that focuses on sequencing specific target regions (amplicons). (novogene.com)

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