Studying the error for HCV amplicon sequencing with the Illumina MiSeq platform

نویسندگان

  • Zoya Dimitrova
  • Lilia Ganova-Raeva
  • Amanda Sue
  • Pavel Skums
  • Natalia Saveleva
  • Yuri Khudyakov
چکیده

Next Generation Sequencing (NGS) is a well established technology for acquisition of vast amount of nucleic acid sequence data at very low cost and high throughput. We aim to provide solid framework for the accurate determination of the viral haplotypes of Hepatitis C virus (HCV) using the Illumina MiSeq platform. To do that, we studied the error rates of sequences generated with the longest available read kits for the MiSeq-v3 (600), applied to bar-coded HCV amplicon libraries of low complexity.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecula...

متن کامل

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at diffe...

متن کامل

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced...

متن کامل

Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.

High-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common "benchtop" sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-o...

متن کامل

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical t...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2016