From: GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure
Tool | Version | Notes |
---|---|---|
nf-core/base | 1.13.3 | The base operating system for all nf-core compatible workflows |
Python3 | 3.9.2 | Used by a variety of custom data wrangling tools |
Aspera | 3.8.1 | Downloads SRA files from NCBI SRA using provided run IDs |
SRAToolkit | 2.10.0 | Downloads SRA files from NCBI using provided SRA Run IDs |
FastQC | 0.11.9 | Generates read quality statistics for FASTQ files |
Trimmomatic | 0.39 | Removes low-quality bases and removes adapter sequences |
STAR | 2.7.9a | Aligns cleaned reads to the reference |
HISAT2 | 2.2.0 | Aligns cleaned reads to the reference |
Salmon | 1.5.2 | Performs quasi-alignment of reads and quantities |
kallisto | 0.46.2 | Performs pseudo-alignment of reads and quantities |
SAMTools | 1.14 | Used for indexing and sorting of BAM files created by HISAT2 |
StringTie | 2.1.7 | Performs gene expression quantification |
MultiQC | 1.11 | Generate a full summary report for the entire workflow |