Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing

Table 1 Differentiation of tested methods by variable

	Method 1	Method 2	Method 3	Method 4	Method 5	Method 6	Method 7
Early vs. Late bead-beating^a	Early	Late	Late	Early	Early	Early	Early
Bead Quantity	150 mg	150 mg	150 mg	75 mg	150 mg	150 mg	150 mg
Phenol vs. No Phenol^b	No phenol	No phenol	Phenol	No phenol	Phenol	No phenol	No phenol
Precipitation Temp/Reagent^c	RT/2-Prop	RT/2-Prop	Cold ETOH	RT/2-Prop	RT/2-Prop	Cold ETOH	RT/2-Prop
Precipitation Salt^d	NaOAc	NaOAc	NaOAc	NaOAc	NaCl	NaOAc	NaOAc
Number of washes	3	3	3	3	3	3	5

^a “Early” bead-beating refers to the timing prior to enzymatic digestion; “Late” bead-beating refers to timing after enzymatic digestion
All Early bead-beating was done in high SDS concentration, see Additional file 1
^b DNA extractions in “no phenol” were extracted as described in Methods with chloroform:isoamyl alcohol (24:1, Tris-saturated)
Extractions in “phenol” were extracted using phenol:chloroform:isoamyl alcohol (25:24:1, Tris-saturated, pH 8.0)
^c Precipitation reagent was either RT 2-Prop (room temperature isopropanol) or Cold ETOH (ethanol). See Additional file 4: Figure S1
^d Precipitation salt was either 3 M sodium acetate (pH 5.2) or 5 M NaCl

ISSN: 1471-2164