Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...

RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. ...

Workflow for Spliced RNAseq data Steps:

• workflow_quality.cwl:
• FastQC (Read Quality Control)
• fastp (Read Trimming)
• STAR (Read mapping)
• featurecounts (transcript read counts)
• kallisto (transcript [pseudo]counts)

RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is CLAN.

RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is BWA-MEM.

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control.