TABLE 1.

Overview of Genefinder, Mykrobe, and Typewriter methods and requirements

Characteristics	Genefinder	Mykrobe (9)	Typewriter (10)
Method	Maps raw reads to list of target alleles using Bowtie	Looks for list of target alleles in de Bruijn assembly graph	Blasts list of target alleles against de novo assembliesa
Input	Fastq file	Fastq file	Genome assembly output (Velvet)
Required homology to declare gene presence/absence	>90% to target allele	Based on kmer recovery: K is minimum percentage expected to be recovered for a gene; K = 0.3 for blaZ, K = 0.6 for fusB and fusC, K = 0.8 otherwise	>90% relative coverage (homology by length) (80% for blaZ)
Required homology to declare SNP	>90% to target: can be modified	100% of 63-kmers required to call a variant present	>90% to target: can be modified
Prediction of stop codons in genes present	Yes	No: there is no assembly	Yes
Reads can be mapped to	Multiple targets	Single target	Single target
Speed/processor	1 to 3 min on laptop with 2.3-GHz processor and 16-GB memoryb	2 min on laptop with 2.3-GHz processor and 16-GB memory	3 h for assemblies on cloud computational system, then a few minutes for BLAST
Sequence quality control	Threshold adjusted if gene has multiple reference sequences or variable level of diversity; can detect potential contamination by comparing avg depth of coverage	Can identify mixtures of different species and same species	Thresholds for N50 and parallel reference-based mapping: nothing reported if below these thresholds

^aUsing blastn for sequence identity and tblast for mutations.

^bGenefinder speed is relative to the number of genes present in the database.