REH Cell Line Multiomic Characterization with Short- and Long-Read Sequencing

Secondary analysis datasets from a multiomic study of the leukemia cell line REH. The data includes depth of coverage, structural variant calls, single nucleotide variant calls, and fusion gene callsets generated from PacBio, Oxford Nanopore, and Illumina sequencing platforms. The repository was created by Mariya Lysenkova Wiklander of Uppsala University.

Use Cases

• Benchmarking structural variant callers based on the provided VCF files from multiple sequencing technologies.
• Comparing coverage depth and copy number variation analyses using the output from samtools and copycat.
• Validating fusion gene detection algorithms using the filtered and raw callset files from both short- and long-read RNA-seq.
• Training machine learning models for variant annotation and filtering using the provided filtered and annotated SNV calls.

Strengths

• Provides multi-platform sequencing data from PacBio, Oxford Nanopore, and Illumina for the same cell line.
• Includes processed outputs from established bioinformatics tools like samtools, sniffles, and multiple fusion callers.
• Offers both raw and filtered variant callsets, facilitating method comparison and quality assessment.

Limitations

• Description metadata is limited; actual data quality requires manual inspection after download.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.

Provenance

Source

Uppsala University

Collection Method

Sequencing and bioinformatic analysis of the REH and GM12878 cell lines.