The invention relates to methods, compositions, devices, systems and kits are described including, without limitation, reagents and mixtures, for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods.

The invention relates to methods, compositions, devices, systems and kits are described including, without limitation, reagents and mixtures, for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods.

This invention provides a process for sequencing nucleic acids using 3 modified deoxynucleotide analogues or 3 modified deoxyinosine triphosphate analogues, and 3 modified dideoxynucleotide analogues having a detectable marker attached thereto.

The present invention provides a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of a pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the pathogen in the extracted nucleic acids, wherein the target locus comprises at least one minor variant associated with drug resistance in the pathogen; d) consecutively sequencing both overlapping nucleic acid strands from a single DNA molecule amplified from the target locus on a Next Generation Sequencing (NGS) platform; e) applying an alignment algorithm to sequencing data from the overlapping nucleic acid strands; and f) performing an analysis of the aligned sequencing data to detect the at least one minor variant and heteroresistant population of the pathogen.

The present invention provides a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of a pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the pathogen in the extracted nucleic acids, wherein the target locus comprises at least one minor variant associated with drug resistance in the pathogen; d) consecutively sequencing both overlapping nucleic acid strands from a single DNA molecule amplified from the target locus on a Next Generation Sequencing (NGS) platform; e) applying an alignment algorithm to sequencing data from the overlapping nucleic acid strands; and f) performing an analysis of the aligned sequencing data to detect the at least one minor variant and heteroresistant population of the pathogen.

An integrated system for sequencing a string of oligo-nucleotides is disclosed, the system includes a sequencer for sequencing a plurality of fragments of the string of oligo-nucleotides via identifying oligo-nucleotides of the fragments one by one and a processor for processing the identified oligo-nucleotides to determine the sequence of the string of oligo-nucleotides and to stop the sequencer from sequencing redundant fragments, where the sequencer and the processor operate in a cycle for each oligo-nucleotide of the fragments.

An integrated system for sequencing a string of oligo-nucleotides is disclosed, the system includes a sequencer for sequencing a plurality of fragments of the string of oligo-nucleotides via identifying oligo-nucleotides of the fragments one by one and a processor for processing the identified oligo-nucleotides to determine the sequence of the string of oligo-nucleotides and to stop the sequencer from sequencing redundant fragments, where the sequencer and the processor operate in a cycle for each oligo-nucleotide of the fragments.

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.

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.

Provided are methods and systems for reducing the time needed for sequencing nucleic acids. The approach relies on detecting formation of nucleotide-specific ternary complexes comprising a polymerase (e.g., a DNA polymerizing enzyme), a primed template nucleic acid molecule, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide, as well as the subsequent next correct nucleotide from a cycle of examining four different nucleotides without requiring chemical incorporation of any nucleotide into the primer.