Research resouces

Bioinformatics pipelines

github.com/dremellab

[High-throughput Alignment and RNA Output Level Detection]

HAROLD

  • Input data: Illumina short-read sequencing data (paired or single end reads; bulk or polyA-selected libraries; stranded or unstranded library synthesis)

  • Designed to be versatile and facilitate analysis of data from multi-organism (infected) samples

  • Compatible with spike-in normalization

  • Uses RNA STAR for transcriptomic mapping and reporting

[Differential Expression Analysis]

DiffEx

  • Input data: Transcriptomic count matrix (from HAROLD)

  • Differential gene expression (DGE) analysis tool using edgeR, DESeq2, and limma

  • Generates interactive Quarto HTML reports

[Chroma]

chroma

forgive the mess, pipeline improvements and feature add-ons are still a work in progress

  • forked from nf-core/atacseq

  • Input data: ATAC-Seq data

  • Designed to be versatile and facilitate analysis of data from multi-organism (infected) samples

  • Can be used with spike-in controls & paired “control” samples

[circularRNA detection & quantitation pipeline]

CHAPLIN

coming soon!

  • Input data: Illumina short-read sequencing data (PE, SE)

  • Adapted for use with small, nonstandard genomes, e.g. viruses

  • Uses CIRCExplorer2, CIRI2 and many other tools in parallel to call and quantify back splice junctions