Fig. 1
From: A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes
Illustration of isolate genome screening workflow, highlighting 3D-printed labware. a Dilution plating on standard media. b Liquid culture in 1.8 mL strip tubes, using 3D-printed compact plate shaker to enhance nutrient and gas mixing. c DNA extraction on Opentrons OT-2 platform, using 3D-printed bead dispenser to aliquot lysis beads directly into liquid culture tubes. d Library prep on Opentrons OT-2 platform, using 3D-printed plate rotator to enhance efficiency of DNA binding to magnetic beads. e DNA sequencing on Illumina platform. f Genome analysis and assembly. g Results from initial rounds of screening, showing samples passing certain QC thresholds at each stage (extraction: 0.1 ng/µL DNA concentration; library prep: 0.5 ng/µL DNA concentration; sequencing: 25 Mbp sequence yield; taxonomy: taxonomy assigned by Sourmash; assembly: high-, medium-, and low-quality assemblies), contaminated assemblies, and unassembled samples. Colored lines connect the same sample through each stage of the chart. Note that even many samples with low DNA extraction concentrations often yielded sufficient sequence data for taxonomic assignment