SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing.
Nucleic Acids Res
; 46(4): e21, 2018 02 28.
Article
in En
| MEDLINE
| ID: mdl-29202193
ABSTRACT
PCR amplicon deep sequencing continues to transform the investigation of genetic diversity in viral, bacterial, and eukaryotic populations. In eukaryotic populations such as Plasmodium falciparum infections, it is important to discriminate sequences differing by a single nucleotide polymorphism. In bacterial populations, single-base resolution can provide improved resolution towards species and strains. Here, we introduce the SeekDeep suite built around the qluster algorithm, which is capable of accurately building de novo clusters representing true, biological local haplotypes differing by just a single base. It outperforms current software, particularly at low frequencies and at low input read depths, whether resolving single-base differences or traditional OTUs. SeekDeep is open source and works with all major sequencing technologies, making it broadly useful in a wide variety of applications of amplicon deep sequencing to extract accurate and maximal biologic information.
Full text:
1
Database:
MEDLINE
Main subject:
Software
/
High-Throughput Nucleotide Sequencing
Language:
En
Journal:
Nucleic Acids Res
Year:
2018
Type:
Article
Affiliation country:
United States