Table 1 Overview of existing pipelines for RNA-seq data analysis
From: transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
Pipeline | Platform | Preprocessing | Assembly | Read mapping | Expression analysis | Functional annotation |
|---|---|---|---|---|---|---|
transXpress | Snakemake | trimmomatic, FastQC, MultiQC | Trinity, rnaSPAdes | bowtie2 (optional) | kallisto, edgeR | BLAST, TargetP, SignalP, TMHMM, BUSCO |
Pincho [8] | Bash, python3 | trimmomatic, Rcorrector, TransRate, CD-HIT | Trinity, rnaSPAdes, BinPacker, IDBA-tran, Velvet-Oases, Shannon, Trans-AbySS, TransLig | HISAT2 | kallisto, RSEM | BLAST, BUSCO, TransRate |
RNAflow [9] | Nextflow | FastQC, MultiQC, fastp, SortMeRNA | Trinity | HISAT2 | DESeq2 | BUSCO, dammit |
Rnnotator (unavailable) [6] | Unknown | Velvet, AMOS | ||||
themira (unavailable) [7] | Unknown | FastXtoolkit, FastX, CAP3 | Velvet-Oases | Blast2GO | ||
nf-core/rnaseq [10] | Nextflow | FastQC, TrimGalore | (None) | STAR, HISAT2 | RSEM, Salmon, DESeq2 | |
Pipeliner [11] | Nextflow | FastQC, MultiQC, TrimGalore | (None) | STAR, HISAT2 | StringTie, HTSeq, featureCounts | |
VIPER [12] | Snakemake | RSeQC | (None) | STAR | Picard, Cufflinks, RSeQC, ComBat, DESeq2, PCA | VarScan, Gostats, GAGE, Pathview, ClusterProfiler, STAR-fusion, TRUST, TIMER, virus contamination detection |
RASflow [13] | Snakemake | TrimGalore, FastQC, MultiQC | (None) | Salmon, HiSAT2 | featureCounts or htseq-count, Qualimap, edgeR, DESeq2 | |
hppRNA [14] | Snakemake | cutadapt, FastQC, PRINSEQ, FASTX-toolkit | (None) | Tophat, bowtie, subread, STAR, HiSAT | Cufflinks, featureCounts, RSEM, eXpress, kallisto, StringTie, ngs.plot, Cuffdiff, DESeq2, EBSeq, edgeR, sleuth, Ballgown | GATK, FusionCatcher |
TRAPLINE [15] | Galaxy | FastxClipper, FastQC, FASTQ, FASTX-toolkit | (None) | Tophat, bowtie | Picard, Cufflinks, Cuffdiff | DAVID, miRanda, BioGRID |
QuickRNAseq [16] | bash, Perl, R | RSeQC | (None) | STAR | featureCounts, RSeQC, edgeR | VarScan |
ARMOR [17] | Snakemake | TrimGalore, FastQC + MultiQC | (None) | Salmon, STAR | edgeR, DRIMSeq | |
BISR-RNAseq [18] | PBS, bash, shiny, R | FastQC + MultiQC | (None) | HiSAT2 | Picard, featureCounts, RSeQC, limma, edgeR | |
RNAseq123 [19] | Bioconductor | (None) | edgeR, limma, glimma |