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Table 1 Containerized software tools used in release v2.0 of GEMmaker

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