Plastid

Plastid is a versatile and powerful Python library that provides nucleotide-resolution analysis of genomics and next-generation sequencing (NGS) data. The primary goal of Plastid is to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. It can be used to represent NGS and other biological data as arrays of values associated with genomic or transcriptomic positions. Plastid is not limited to specific experimental regimes or analytical workflows, making it a widely applicable tool for researchers in the field of genomics and bioinformatics.

Plastid offers a range of configurable tools to convert data from various sources into arrays. It also includes numerous tools to manipulate genomic features, such as spliced transcripts, with nucleotide precision. Furthermore, Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, which frees users from having to perform these complex calculations manually.

One of the key features of Plastid is its data models, which use consistent and familiar biological idioms. This makes it easy for even beginners to develop sophisticated analytical workflows with minimal effort. Plastid has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of ORF-RATER, an ORF annotation tool, and can be readily adapted to novel NGS assays.