Table 2.
14 tools in common between the top 20 Nextflow tools and the top 20 Snakemake tools. # NF: Number of Nextflow processors in which they appear, # SM: Number of Snakemake processors in which they appear. Category: (i) genomic toolkits (GT), (ii) sequence mappers (MAP), (iii) quality control (QC) tools, and (iv) domain-specific tools (DST).
| Tool | # NF | # SM | Category |
|---|---|---|---|
| Samtools | 2841 | 2045 | GT |
| BEDTools[43] | 384 | 603 | GT |
| BCFtools[44] | 929 | 360 | GT |
| BWA | 412 | 356 | MAP |
| GATK | 1067 | 269 | GT |
| FastQC[45] | 770 | 236 | QC |
| Bowtie[46] | 243 | 177 | MAP |
| STAR[47] | 234 | 152 | MAP |
| MultiQC[48] | 707 | 137 | QC |
| Minimap2[49] | 149 | 137 | MAP |
| Picard | 269 | 137 | GT |
| seqtk | 96 | 94 | GT |
| Cutadapt[50] | 80 | 81 | GT |
| QIIME[51] | 207 | 90 | DST |