Table 1.
Variant calling pipelines tested in this study.
| Pipelinea | Approach | Reference-based | Input data (file format)b | Read mapper | Variant caller | Reference(s) and in-depth pipeline descriptions |
|---|---|---|---|---|---|---|
| CFSAN | Read mapping | Yes | PE reads (fastq) | Bowtie2 | Varscan | http://snp-pipeline.readthedocs.io/en/latest/ |
| Freebayes | Read mapping | Yes | PE reads (fastq) | BWA MEM | Freebayes | https://github.com/lmc297/SNPBac |
| kSNP3 | k-mer based | No | Contigs (fasta) | Not applicable | kSNP3 | https://sourceforge.net/projects/ksnp/files/ |
| LYVE-SET | Read mapping | Yes | PE reads (fastq) | SMALT | Varscan | https://github.com/lskatz/lyve-SET |
| Parsnp | Core genome alignment | Yes | Contigs (fasta) | Not applicable | Parsnp | http://harvest.readthedocs.io/en/latest/content/parsnp.html |
| Samtools | Read mapping | Yes | PE reads (fastq) | BWA MEM | Samtools/Bcftools | https://github.com/lmc297/SNPBac |
a
CFSAN, U.S. Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition SNP pipeline; LYVE-SET, U.S. Centers for Disease Control and Prevention (CDC) Listeria, Yersinia, Vibrio, and Enterobacteriaceae SNP Extraction Tool.
b
PE reads, Illumina paired-end reads.