Methods and systems for decreasing amplification bias and primer-dimer formation in amplification reactions and for amplifying a plurality of target polynucleotides from a sample in a single reaction and for sequencing the target polynucleotides where samples can include forensic samples and where target polynucleotides can include identity- or ancestry-informative markers, short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Methods of determining a nucleotide spacer sequence for disrupting primer dimer formation can include: receiving a set of primer sequences; determining a plurality of candidate spacers between an adapter sequence and a gene-specific portion of the primer sequence, the determined plurality of candidate spacers comprises sequences that disrupt stable interactions between sequences of the set of primer sequences; ranking candidate spacers that meet a predetermined threshold value of stable interactions in the extension sequences; and outputting a set of the ranked spacers that meet the predetermined threshold.

Methods and systems for decreasing amplification bias and primer-dimer formation in amplification reactions and for amplifying a plurality of target polynucleotides from a sample in a single reaction and for sequencing the target polynucleotides where samples can include forensic samples and where target polynucleotides can include identity- or ancestry-informative markers, short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Methods of determining a nucleotide spacer sequence for disrupting primer dimer formation can include: receiving a set of primer sequences; determining a plurality of candidate spacers between an adapter sequence and a gene-specific portion of the primer sequence, the determined plurality of candidate spacers comprises sequences that disrupt stable interactions between sequences of the set of primer sequences; ranking candidate spacers that meet a predetermined threshold value of stable interactions in the extension sequences; and outputting a set of the ranked spacers that meet the predetermined threshold.

The invention relates to control compositions for sequencing and for chemical analyses, such as analytical chemistry analyses. More particularly, the invention relates to control compositions for sequencing and for chemical analyses having at least one barcode sequence fragment and at least one universal sequence fragment, and to methods of their use.

The invention relates to control compositions for sequencing and for chemical analyses, such as analytical chemistry analyses. More particularly, the invention relates to control compositions for sequencing and for chemical analyses having at least one barcode sequence fragment and at least one universal sequence fragment, and to methods of their use.

Methods for enhancing specificity of an analyte binding moiety or probe oligonucleotide to an analyte are provided herein. For example, methods provided herein include blocking a capture binding domain, thereby preventing hybridization to the capture domain of the capture probe affixed to a substrate. Further methods include releasing the block from the capture binding domain, thereby allowing the capture binding domain to specifically bind to the capture domain of the capture probe on the substrate.

Methods for enhancing specificity of an analyte binding moiety or probe oligonucleotide to an analyte are provided herein. For example, methods provided herein include blocking a capture binding domain, thereby preventing hybridization to the capture domain of the capture probe affixed to a substrate. Further methods include releasing the block from the capture binding domain, thereby allowing the capture binding domain to specifically bind to the capture domain of the capture probe on the substrate.

The present disclosure provides methods and kits for tracking nucleic acid target origin by barcode tagging of the targets when they break into smaller fragments. Nucleic acid targets are captured in vitro by clonally localized nucleic acid barcode templates on a solid support. Millions of nucleic acid targets can be processed simultaneously in a massively parallel fashion without additional partition. These captured targets are broken into small fragments, and a target specific barcode sequence is tagged on each fragment as an identification of their original target. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing.

The present disclosure provides methods and kits for tracking nucleic acid target origin by barcode tagging of the targets when they break into smaller fragments. Nucleic acid targets are captured in vitro by clonally localized nucleic acid barcode templates on a solid support. Millions of nucleic acid targets can be processed simultaneously in a massively parallel fashion without additional partition. These captured targets are broken into small fragments, and a target specific barcode sequence is tagged on each fragment as an identification of their original target. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing.

Provided herein are methods of releasing an extended capture probe from a substrate and uses of the same.

Provided herein are methods of releasing an extended capture probe from a substrate and uses of the same.