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Fig. 3 | BMC Research Notes

Fig. 3

From: Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error

Fig. 3

Comparison of 16 combinations of reference-guided sequence assemblers and SNP callers. Genomic DNA from the Listeriosis Reference Service for Canada’s (LRS) Listeria monocytogenes strain HPB5622 culture was indexed and sequenced, yielding a high (~79-fold) and a low (~eightfold) coverage datasets. The resulting reads were aligned with the Burrows-Wheeler Aligner (BWA), MOSAIK, Novoalign, and SMALT using both L. monocytogenes strain 08-5578 (a) and EGD-e (b) chromosome sequences obtained from the National Center for Biotechnology Information (NCBI) archive as references. The NCBI strain 08-5578 chromosome sequence differs from HPB5622 at three nucleotide positions, while the EGD-e chromosome sequence differs at 24,890 nucleotide positions. Four SNP-callers (BCFtools [BCF], FreeBayes, UnifiedGenotyper [UGT], and VarScan) were used to identify nucleotide differences

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