GUESSmyLT

GUESSmyLT identifies the RNA-Seq library type of single-end and paired-end read files to determine strandedness, read orientation, and related library attributes for improved mapping and transcriptome assembly.

Key Features:

• Library type attributes: Determines single-end versus paired-end status, strandedness (stranded or unstranded), 5' versus 3' orientation, paired-end inward versus outward orientation, and strand origin of paired reads.
• Input data compatibility: Accepts mapped reads and raw reads, and operates with or without gene annotation and with or without a reference genome.
• Mapping and annotation usage: Leverages read mapping and gene annotation data to characterize read orientation and strand origin.
• Integrated tools: Incorporates Bowtie2 for alignment, Trinity for de novo transcriptome assembly, and BUSCO for gene set completeness assessment within its workflow.
• Workflow engine: Implements analysis steps within a Snakemake pipeline and performs a subsequent inference step to predict the library type.

Scientific Applications:

• Improved read mapping: Uses inferred library type to improve read alignment to a reference assembly or genome.
• Transcriptome assembly: Informs de novo transcriptome assembly by providing strand and orientation information.
• Ambiguous read resolution: Resolves ambiguous reads by considering relative orientation and strand origin.
• Metadata recovery: Infers library information for datasets that lack or mislabel sequencing metadata.

Methodology:

Integrates Bowtie2 for aligning reads to a reference genome, Trinity for de novo transcriptome assembly, and BUSCO for gene set completeness within a Snakemake pipeline, followed by an inference step to predict the library type.