Nadin Rohland and David Reich developed a cost-effective, high-throughput DNA sequencing library method for multiplexed target capture. This method allows the production of sequencing libraries in a single day at a cost of about $15 per sample. The libraries are effective for low-pass whole-genome sequencing and for enriching pools of approximately 100 individually barcoded samples for a subset of the genome without significant loss in target capture efficiency. The method was tested on about 2000 samples from a prostate cancer study. The method reduces sequencing costs and increases throughput by parallelizing library preparation in 96-well plates, reducing enzyme volumes, using inexpensive paramagnetic beads for size selection and buffer exchange, and automation. Internal barcodes are directly ligated to sheared DNA fragments, allowing highly multiplexed sample pooling prior to target enrichment. This approach enables the simultaneous sequencing of up to 95 barcoded samples without substantial reduction in capture efficiency. The method is particularly effective for projects requiring a modest amount of sequencing per sample, such as low-pass sequencing of human genomes, microbial sequencing, and target capture of human exomes and smaller genomic targets. It is less ideal for deep sequencing of large genomes, such as the human genome at 30×, where sequencing costs are high enough to justify using libraries with lower duplication rates. The method was tested on 2000 prostate cancer samples, with libraries enriched for a 2.2-Mb subset of the genome. The results showed high-quality data with good polymorphism discovery. The method was also tested on 40 human libraries and 12 E. coli strains, demonstrating its effectiveness for whole-genome sequencing and microbial sequencing. The method is cost-effective, with reagent costs of about $9 per sample, technician time of $3 per sample, and capital equipment costs of about $3 per sample. It is suitable for academic laboratories to generate thousands of barcoded libraries at a cost one to two orders of magnitude less than commercial library preparation. The method is adaptable to various sequencing technologies and can be used for different applications, including whole-genome sequencing, microbial sequencing, and target capture. The method has been published in Genome Research and is available for further study and application.Nadin Rohland and David Reich developed a cost-effective, high-throughput DNA sequencing library method for multiplexed target capture. This method allows the production of sequencing libraries in a single day at a cost of about $15 per sample. The libraries are effective for low-pass whole-genome sequencing and for enriching pools of approximately 100 individually barcoded samples for a subset of the genome without significant loss in target capture efficiency. The method was tested on about 2000 samples from a prostate cancer study. The method reduces sequencing costs and increases throughput by parallelizing library preparation in 96-well plates, reducing enzyme volumes, using inexpensive paramagnetic beads for size selection and buffer exchange, and automation. Internal barcodes are directly ligated to sheared DNA fragments, allowing highly multiplexed sample pooling prior to target enrichment. This approach enables the simultaneous sequencing of up to 95 barcoded samples without substantial reduction in capture efficiency. The method is particularly effective for projects requiring a modest amount of sequencing per sample, such as low-pass sequencing of human genomes, microbial sequencing, and target capture of human exomes and smaller genomic targets. It is less ideal for deep sequencing of large genomes, such as the human genome at 30×, where sequencing costs are high enough to justify using libraries with lower duplication rates. The method was tested on 2000 prostate cancer samples, with libraries enriched for a 2.2-Mb subset of the genome. The results showed high-quality data with good polymorphism discovery. The method was also tested on 40 human libraries and 12 E. coli strains, demonstrating its effectiveness for whole-genome sequencing and microbial sequencing. The method is cost-effective, with reagent costs of about $9 per sample, technician time of $3 per sample, and capital equipment costs of about $3 per sample. It is suitable for academic laboratories to generate thousands of barcoded libraries at a cost one to two orders of magnitude less than commercial library preparation. The method is adaptable to various sequencing technologies and can be used for different applications, including whole-genome sequencing, microbial sequencing, and target capture. The method has been published in Genome Research and is available for further study and application.