getSequenceInfo

getSequenceInfo retrieves sequence data from public repositories such as GenBank, RefSeq, and the European Nucleotide Archive and computes basic assembly metrics for downstream genomic analyses.

Key Features:

• Data Access and Retrieval: Queries GenBank, RefSeq, and the European Nucleotide Archive using criteria such as kingdom, species, and date of release to retrieve sequence records and metadata.
• Organizational Capabilities: Separates genetic elements by organizing chromosomes, plasmids, and other components into distinct folders.
• Statistical Analysis: Calculates GC content for queried assemblies and computes an empirically designed nucleotide ratio to generate a "NucleScore" as an assembly evaluation metric.
• Output Formats: Exports sequence and metadata results in FASTA, FASTQ, Excel/TSV, and HTML formats.
• Supplementary Tools: Includes additional utilities to support a range of sequence analysis tasks.

Scientific Applications:

• Genomic data retrieval: Provides curated sequence records and assembly metrics to support comparative genomics and assembly assessment.
• Metadata enrichment: Supplies contextual metadata such as country of origin and isolation date to inform epidemiological and population studies.
• Education and programmatic access: Enables pedagogical use and programmatic access to genomic data for reproducible analyses.

Methodology:

Programmatic access to sequence databases, performing queries based on user-defined parameters, and organizing retrieved data into a structured format.