HTSinfer

HTSinfer infers metadata directly from bulk Illumina RNA-sequencing data using genome sequence information and diagnostic genes to determine library characteristics.

Key Features:

• Library Source Inference: Identifies the organism from which sequenced reads were derived using genome sequence information and diagnostic genes.
• Library Type Inference: Determines the type of sequencing library from the RNA-Seq data.
• Read Orientation Inference: Infers the relative orientation of paired-end reads.
• Adapter Sequence Detection: Identifies 3' adapter sequences present in the library.
• Read Length Statistics: Calculates read length statistics from the input data.
• Modular Architecture: Written in a modular manner to enable community contributions and extension to additional metrics, experiment types, or sequencing platforms.

Scientific Applications:

• Metadata Verification: Verifies the consistency and completeness of manually entered metadata for sequencing libraries deposited in repositories such as the Sequencing Read Archive.
• Data Reuse Facilitation: Enables accurate secondary analyses of publicly available RNA-Seq data by correcting or completing erroneous or incomplete metadata.
• Library Quality Control: Rapidly determines key library characteristics for quality assessment before downstream analysis.

Methodology:

HTSinfer leverages genome sequence information and diagnostic genes to infer library characteristics directly from bulk RNA-sequencing data generated on Illumina platforms.