Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

High-throughput production of modified microbes is achieved through optimization of directed build graph data structures representing biological workflows. Portions of otherwise unrelated workflows may be combined where they share common biological reaction steps, and processed by a genetic manufacturing facility to take advantage of operational efficiencies. Workflows may be mapped to physical laboratory equipment in a manner that optimizes material transfers. Different automated platforms running different machines in different languages are coordinated in a device-agnostic and language-agnostic manner.

High-throughput production of modified microbes is achieved through optimization of directed build graph data structures representing biological workflows. Portions of otherwise unrelated workflows may be combined where they share common biological reaction steps, and processed by a genetic manufacturing facility to take advantage of operational efficiencies. Workflows may be mapped to physical laboratory equipment in a manner that optimizes material transfers. Different automated platforms running different machines in different languages are coordinated in a device-agnostic and language-agnostic manner.

Disclosed is a computer-implemented method for determining a measure correlated to the probability that two mutated sequence reads derive from the same sequence comprising mutations. The method comprises receiving mutated sequence reads each corresponding to a subsequence of a sequence comprising mutations compared to a sequence not comprising mutations, applying a common minimizer function to each mutated sequence read, to determining minimizers for each mutated sequence read, determining positions of the one or more minimizers in each mutated sequence read, determining positions of mutations in each mutated sequence read, and for at least two mutated sequence reads with a common minimizer, counting the number of mutations with matching position and/or mismatching position when the respective minimizers are aligned. Also disclosed is a corresponding method for determining at least a portion of a sequence of at least one target template nucleic acid molecule.

Disclosed is a computer-implemented method for determining a measure correlated to the probability that two mutated sequence reads derive from the same sequence comprising mutations. The method comprises receiving mutated sequence reads each corresponding to a subsequence of a sequence comprising mutations compared to a sequence not comprising mutations, applying a common minimizer function to each mutated sequence read, to determining minimizers for each mutated sequence read, determining positions of the one or more minimizers in each mutated sequence read, determining positions of mutations in each mutated sequence read, and for at least two mutated sequence reads with a common minimizer, counting the number of mutations with matching position and/or mismatching position when the respective minimizers are aligned. Also disclosed is a corresponding method for determining at least a portion of a sequence of at least one target template nucleic acid molecule.

Provided herein are methods for accurately determining the alleles present at a locus that is broadly applicable to any locus, including highly polymorphic loci such as HLA loci, BGA loci and HV loci. Embodiments of the disclosed methods are useful in a wide range of applications, including, for example, organ transplantation, personalized medicine, diagnostics, forensics and anthropology.

Provided herein are methods for accurately determining the alleles present at a locus that is broadly applicable to any locus, including highly polymorphic loci such as HLA loci, BGA loci and HV loci. Embodiments of the disclosed methods are useful in a wide range of applications, including, for example, organ transplantation, personalized medicine, diagnostics, forensics and anthropology.

The efficiency of polymer synthesis is increased by reducing the number of monomer addition cycles needed to create a set of polymer strands. The number of cycles depends on the sequences of the polymer strands and the order in which each type of monomer is made available for addition to the growing strands. Efficiencies are created by grouping the polymer strands into batches such that all the strands in a batch require a similar number of cycles to synthesize. Efficiencies are also created by selecting an order in which the monomers are made available for addition to the growing polymer strands in a batch. Both techniques can be used together. With these techniques, the number of cycles of monomer addition and commensurate reagent use may be reduced by over 10% as compared to naïve synthesis techniques.

The efficiency of polymer synthesis is increased by reducing the number of monomer addition cycles needed to create a set of polymer strands. The number of cycles depends on the sequences of the polymer strands and the order in which each type of monomer is made available for addition to the growing strands. Efficiencies are created by grouping the polymer strands into batches such that all the strands in a batch require a similar number of cycles to synthesize. Efficiencies are also created by selecting an order in which the monomers are made available for addition to the growing polymer strands in a batch. Both techniques can be used together. With these techniques, the number of cycles of monomer addition and commensurate reagent use may be reduced by over 10% as compared to naïve synthesis techniques.