Atria: an ultra-fast and accurate trimmer for adapter and quality trimming.
GigaByte
; 2021: gigabyte31, 2021.
Article
em En
| MEDLINE
| ID: mdl-36967729
ABSTRACT
With advances in next-generation sequencing, adapters attached to reads and low-quality bases directly and implicitly hinder downstream analysis. For example, they can produce false-positive single nucleotide polymorphisms (SNP), and generate fragmented assemblies. There is a need for a fast trimming algorithm to remove adapters precisely, especially in read tails with relatively low quality. Here, we present Atria, a trimming program that matches the adapters in paired reads and finds possible overlapped regions using a fast and carefully designed byte-based matching algorithm (O (n) time with O (1) space). Atria also implements multi-threading in both sequence processing and file compression and supports single-end reads. Compared with other trimmers, Atria performs favorably in various trimming and runtime benchmarks of both simulated and real data. We also provide a fast and lightweight byte-based matching algorithm, which can be used in various short-sequence matching applications, such as primer search and seed scanning before alignment.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Idioma:
En
Revista:
GigaByte
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Canadá