ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data.
Bioinformatics
; 38(1): 257-260, 2021 12 22.
Article
em En
| MEDLINE
| ID: mdl-34293115
ABSTRACT
MOTIVATION DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. RESULTS:
Here, we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. AVAILABILITY AND IMPLEMENTATION ModPhred is available at https//github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Nanoporos
/
Sequenciamento por Nanoporos
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Espanha