Aug 18, 2012

Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

PloS One
Brant C Faircloth, Travis C Glenn

Abstract

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (max(count) = 7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially av...Continue Reading

  • References48
  • Citations78

Citations

Mentioned in this Paper

Real-Time Polymerase Chain Reaction
Twitter Messaging
Polymerase
Complement System Proteins
Genome
Gene Deletion Abnormality
DNA Library
Gene Amplification Technique
Binary Encoding
Computer Programs and Programming

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