Table 4.
License type, as well as de novo assembly and allele calling pipelines recommended by developers of cgMLST workflows compared in the present study to assess precision of Listeria monocytogenes cgMLST typing. N/A stands for not applicable
| cgMLST workflow (version) | License type | Recommended assembly pipeline (version) | Recommended allele calling pipeline (strategy or version) | Reference |
|---|---|---|---|---|
| BIGSdb (N/A) | open source | AlienTrimmer (2.0)-, Musket (1.1)-and SPAdes (3.15.0)-based fq2dna (21.06) | BLASTN-based BIGSdb (alignment) | [24] |
| INNUENDO (N/A) | open source | Trimmomatic (0.36)-, Pilon (1.18)- and SPAdes (3.9.0)- based INNUca (4.2.2) | Prodigal- (ORF discovery) and BLASTP-based (alignment) chewBBACA (2.6.0) | [14, 49] |
| GENPAT (N/A) | open source | Trimmomatic (0.36)- and SPAdes (3.11.1)-based pipeline | Prodigal- (ORF discovery) and BLASTP-based (alignment) chewBBACA (2.6.0) | [14, 57, 58] |
| SeqSphere (6.0.2) | commercial | FastQC (0.11.7)- and SPAdes (3.11.1)-based pipeline | BLASTN-based SeqSphere (alignment) | [12, 59, 67] |
| Bionumerics (7.6.3) | commercial | SPAdes (3.7.1)-based pipeline | BLASTN-based assembly-based and -free algorithms (alignments) | [17, 20, 61, 62] |
| MentaLiST (1.0.0) | open source | N/A (i.e. assembly free) | stringMLST principle-based MentaLiST (kmer counting) | [13, 19] |