MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
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 ...
Type: Shell Script
Creators: Tracy Chew, Rosemarie Sadsad, Georgina Samaha, Cali Willet
Submitter: Tracy Chew
DownloadRNASeq-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. ...
Type: Shell Script
Creators: Georgina Samaha, Rosemarie Sadsad, Tracy Chew, Matthew Downton, Andrey Bliznyuk, Rika Kobayashi, Ben Menadue, Ben Evans
Submitter: Tracy Chew
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.
