Software

Software

Genboree

Genboree is a web-based platform for multi-omic research and data analysis using the latest bioinformatics tools.

genboree

Genboree Workbench Long RNA-Seq analysis pipeline

The long RNA-Seq pipeline uses several well-established tools, including FastQC, Bowtie, Samtools, and specific modules from RSEQtools. FastQC performs a quality check on the sequence reads, Bowtie maps the reads to the reference genome, and Samtools is used to post-process the aligned reads. Downstream analysis utilizes RSEQtools modules to perform gene-expression quantification, visualize signal tracks of mapped reads, calculate mapping bias, and compute annotation coverage.

exceRpt - Genboree Workbench Small RNA-seq analysis pipeline

At its core, the small RNA-seq pipeline utilises the sRNAbench software tool, which is itself based on miRanalyzer and Bowtie for mapping and profiling various small RNA libraries including miRNAs from miRBase, tRNAs from gtRNAdb, piRNAs from RNAdb, snoRNAs from snoRNA-LBME-db, and snRNAs and other RNA sequences from RFam. Abundance estimates for each of the requested libraries are output, as are a variety of quality control metrics such as read-length distributions, summaries of reads mapped to each library, and detailed mapping information for each read mapped to each library.

exceRpt Analysis Pipeline Flowchart

Data Use Cases

The DMRR has developed several use cases based on consortium members' datasets and publications. The purpose of these use cases is to highlight the software tools developed by the DMRR, with the long-term goal that all future datasets generated by the consortium can be analyzed reproducibly and compared to each other.

  • Use Case 1: Exogenous exRNA (pdf, pptx, article)
  • Use Case 2: exRNA in Alzheimer's and Parkinson's Diseases
    • Use Case 2 Part 1: The exceRpt Pipeline (pdf, pptx, data, article)
    • Use Case 2 Part 2: The exRNA Atlas, DEseq and exceRpt pipelines, Vesiclepedia, and Pathway Analysis (pdf, data, article)
  • Use Case 3: Biomarker Potential and Limitations of Circulating miRNA (pdf, pptx, data, article)