Abstract: Described herein are methods and systems for improving nucleic acid sequencing read quality. An exemplary method comprises receiving, at one or more processors, sequencing data comprising a plurality of sequencing reads; filtering the sequencing data, using the one or more processors, to remove sequencing reads for which an absence of an incorporated nucleotide was detected at three or more consecutive sequencing flow steps, thereby generating filtered sequencing data; determining, using the one or more processors, for each sequencing flow step of each sequencing read, a read quality metric based on one or more homopolymer probability values other than a highest homopolymer probability value; and trimming the terminus of one or more sequencing reads in the sequencing data based on the read quality metrics for a respective sequencing read, thereby generating trimmed sequencing data.

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.

Abstract: Controlling an etch process applied to a multi-layered structure, by calculating a spectral derivative of reflectance of an illuminated region of interest of a multi-layered structure during an etch process applied to the multi-layered structure, identifying in the spectral derivative a discontinuity that indicates that an edge of a void formed by the etch process at the region of interest has crossed a layer boundary of the multi-layered structure, determining that the crossed layer boundary corresponds to a preselected layer boundary of the multi-layered structure, and applying a predefined control action to the etch process responsive to determining that the crossed layer boundary corresponds to the preselected layer boundary of the multi-layered structure.

Abstract: Described herein are methods of sequencing a polynucleotide and methods of analyzing sequencing data obtained from such sequencing methods. The sequencing methods can include accelerated primer extension through a region of the polynucleotide using labeled nucleotides provided according to a flow order, measuring a signal from labeled nucleotides incorporated into the primer, and determining distance information that indicates the length of the region using the measured signal.

Abstract: Described herein are methods synchronizing sequencing primers within a sequencing cluster and methods of generating long-range sequencing reads. The methods can include hybridizing primers to polynucleotide copies within a sequencing cluster; extending the primers through a first region of the polynucleotide copies using labeled nucleotides according to a sequencing flow order; extending the primers through a second region of the polynucleotide copies using one or more re-phasing flow steps that each include at least two different types of nucleotide bases; and extending the primers through a third region of the polynucleotide copies using labeled nucleotides according to the sequencing cycle. The rephasing flow steps may be initiated after a predetermined number of sequencing flow steps, after a measured sequencing signal strength falls below a predetermined sequencing signal strength threshold, or a measured sequencing signal-to-noise ratio falls below a sequencing signal-to-noise ratio threshold.

Abstract: The present disclosure provides methods, systems, and media for accurate and efficient estimation of a genome of a genus. The methods and systems described herein may be used to accurately determine a base sequence of a polynucleotide. Additionally, the methods and systems may be used to identify base variants of a polynucleotide.

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or more match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.

Abstract: The present disclosure provides methods, systems, and media for accurate and efficient estimation of a genome of a genus.

Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

Abstract: The present disclosure provides methods, systems, and media for accurate and efficient estimation of a genome of a genus.

Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

Abstract: A process control method for manufacturing semiconductor devices, including determining a quality metric of a production semiconductor wafer by comparing production scatterometric spectra of a production structure of the production wafer with reference scatterometric spectra of a reference structure of reference semiconductor wafers, the production structure corresponding to the reference structure, the reference spectra linked by machine learning to a reference measurement value of the reference structure, determining a process control parameter value (PCPV) of a wafer processing step, the PCPV determined based on measurement of the production wafer and whose contribution to the PCPV is weighted with a first predefined weight based on the quality metric, and based on a measurement of a different wafer and whose contribution to the PCPV is weighted with a second predefined weight based on the quality metric, and controlling, with the PCPV, the processing step during fabrication.

Abstract: Controlling an etch process applied to a multi-layered structure, by calculating a spectral derivative of reflectance of an illuminated region of interest of a multi-layered structure during an etch process applied to the multi-layered structure, identifying in the spectral derivative a discontinuity that indicates that an edge of a void formed by the etch process at the region of interest has crossed a layer boundary of the multi-layered structure, determining that the crossed layer boundary corresponds to a preselected layer boundary of the multi-layered structure, and applying a predefined control action to the etch process responsive to determining that the crossed layer boundary corresponds to the preselected layer boundary of the multi-layered structure.

Abstract: The present disclosure provides methods, systems, and media for accurate and efficient estimation of a genome of a genus.

Abstract: Controlling an etch process applied to a multi-layered structure, by calculating a spectral derivative of reflectance of an illuminated region of interest of a multi-layered structure during an etch process applied to the multi-layered structure, identifying in the spectral derivative a discontinuity that indicates that an edge of a void formed by the etch process at the region of interest has crossed a layer boundary of the multi-layered structure, determining that the crossed layer boundary corresponds to a preselected layer boundary of the multi-layered structure, and applying a predefined control action to the etch process responsive to determining that the crossed layer boundary corresponds to the preselected layer boundary of the multi -layered structure.

Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

Abstract: A process control method for manufacturing semiconductor devices, including determining a quality metric of a production semiconductor wafer by comparing production scatterometric spectra of a production structure of the production wafer with reference scatterometric spectra of a reference structure of reference semiconductor wafers, the production structure corresponding to the reference structure, the reference spectra linked by machine learning to a reference measurement value of the reference structure, determining a process control parameter value (PCPV) of a wafer processing step, the PCPV determined based on measurement of the production wafer and whose contribution to the PCPV is weighted with a first predefined weight based on the quality metric, and based on a measurement of a different wafer and whose contribution to the PCPV is weighted with a second predefined weight based on the quality metric, and controlling, with the PCPV, the processing step during fabrication.

Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.