The invention discloses a method for identifying the bacterial species and key functional genes thereof involved in antimony reduction in the soil. After consuming the original substrate by starvation culture, the sole metabolic substrate is added and the sole electron acceptor Sb(V) is provided, so that there is only one dominant electron exchange process in the system. The microorganisms metabolize and oxidize the organic substrate while coupling with the reduction of antimony, so that Sb(V) gets electrons and is reduced to Sb(III). The present invention observes the Sb(V) reduction in an anaerobic culture system of paddy soil under Sb(V) stress, and uses DNA-SIP technology to identify the phylogenic information of microorganisms that can drive the Sb(V) reduction in the culture system. The invention explores the metabolism of the antimony-reducing microorganisms and the key functional microorganisms in the paddy soil, which has great significance for understanding the antimony reduction process driven by the microorganisms, and cognizing the antimony reduction bacteria and the key functional genes.

The invention discloses a method for identifying the bacterial species and key functional genes thereof involved in antimony reduction in the soil. After consuming the original substrate by starvation culture, the sole metabolic substrate is added and the sole electron acceptor Sb(V) is provided, so that there is only one dominant electron exchange process in the system. The microorganisms metabolize and oxidize the organic substrate while coupling with the reduction of antimony, so that Sb(V) gets electrons and is reduced to Sb(III). The present invention observes the Sb(V) reduction in an anaerobic culture system of paddy soil under Sb(V) stress, and uses DNA-SIP technology to identify the phylogenic information of microorganisms that can drive the Sb(V) reduction in the culture system. The invention explores the metabolism of the antimony-reducing microorganisms and the key functional microorganisms in the paddy soil, which has great significance for understanding the antimony reduction process driven by the microorganisms, and cognizing the antimony reduction bacteria and the key functional genes.

A method for storing, by a processor, a genomic graph representing a plurality of individual genomes, including: storing a linear representation of a reference genome in a data storage; receiving a first genome; identifying variations in the first genome from the reference genome; generating graph edges for each variation in the first genome from the reference genome; generating for each generated graph edge: an edge identifier that uniquely identifies the current edge in the genome graph; a start edge identifier that identifies the edge from which the current edge branches out; a start position that indicates the position on the start edge that serves as an anchoring point for the current edge; an end edge identifier that identifies the edge into which the current edge joins in; an end position that indicates the position on the end edge that serves as an anchoring point for the current edge; and a sequence indicating the nucleotide sequence of the current edge; and storing the edge identifier, start edge identifier, start position, end edge identifier, end edge position, and sequence for each generated graph edge in the data storage. Based on this genome graph data structure, we further propose a scheme for specifying a path, which may traverse one or more edges, and the ways to extend existing genomic data formats such as SAM, VCF and MPEG-G to support the use of genome graph reference using our proposed coordinate system.

Systems and methods for determining a sequence of at least a portion of a target polymer from a subject are provided. A dataset that comprises one or more image files is obtained. A combined plurality of localizations based at least in part on each respective plurality of fluorophore localizations is determined for each image file in the one or more image files. Each localization in the combined plurality of localizations includes a target polymer position identity and a spatial location. The plurality of localizations are segmented into one or more target polymer strands. Each target polymer strand corresponds to a respective subset of localizations and target polymer position identities. A respective target polymer sequence is assembled using each subset of localizations for each target polymer strand, thereby providing a set of target polymer sequences.

Systems and methods for determining a sequence of at least a portion of a target polymer from a subject are provided. A dataset that comprises one or more image files is obtained. A combined plurality of localizations based at least in part on each respective plurality of fluorophore localizations is determined for each image file in the one or more image files. Each localization in the combined plurality of localizations includes a target polymer position identity and a spatial location. The plurality of localizations are segmented into one or more target polymer strands. Each target polymer strand corresponds to a respective subset of localizations and target polymer position identities. A respective target polymer sequence is assembled using each subset of localizations for each target polymer strand, thereby providing a set of target polymer sequences.

In one aspect, a method is disclosed wherein an artificial intelligence (AI) enabled automated flow synthesis platform is configured to generate optimized synthesizing recipes which enable a sequence to be synthesized using an automated flow process. The method includes receiving a synthesizing recipe including parameters used during the automated flow process to synthesize the sequence, receiving spectral data from detectors monitoring the automated flow process in a reaction chamber, where the spectral data corresponds to a reaction point in the automated flow process, and determining, based on indicators associated with the spectral data, characteristics of a chemical reaction at the reaction point in the automated flow process. An artificial intelligence engine determines the chemical reaction. The method includes associating, based on the spectral data, the synthesizing recipe with the chemical reaction.

In one aspect, a method is disclosed wherein an artificial intelligence (AI) enabled automated flow synthesis platform is configured to generate optimized synthesizing recipes which enable a sequence to be synthesized using an automated flow process. The method includes receiving a synthesizing recipe including parameters used during the automated flow process to synthesize the sequence, receiving spectral data from detectors monitoring the automated flow process in a reaction chamber, where the spectral data corresponds to a reaction point in the automated flow process, and determining, based on indicators associated with the spectral data, characteristics of a chemical reaction at the reaction point in the automated flow process. An artificial intelligence engine determines the chemical reaction. The method includes associating, based on the spectral data, the synthesizing recipe with the chemical reaction.

The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.

Provided herein are high-throughput sequencing methods to study the diversity and functionality of lymphocyte receptor chains and pairing of the same. Specifically, the methods provided herein are used to identify with confidence one or more lymphocyte receptor chain pairs in a sample, for example one or more functional chain pairs.