Fast-NA for threat detection in high-throughput sequencing

A system for analyzing an output of a sequencer in real time, the system comprising:

• a memory;
• at least one database configured to store target signature snippets;
• at last one processor coupled to the memory and to the at least one database and configured to:
• identify a group of genetic targets, each genetic target being a target organism to be detected in a sample;
• determine a plurality of sets of one or more target signature snippets responsive to identifying the group of genetic targets, each set of one or more target signature snippet being derived from a genetic sequence of a respective genetic target of the group of genetic targets, wherein each of the plurality of sets of one or more target signature snippets (i) having previously been classified as corresponding to a respective genetic target of the group of genetic targets, (ii) 1 being derived from a genetic sequence of the respective genetic target, and (iii) do not correspond to snippets derived from a plurality of non-target organism sequences;
• filter the plurality of sets of one or more target signature snippets to identify a set of one or more universal target signature snippets, wherein the set of one or more universal target signature snippets consist of one or more target signature snippets that belong to each of the plurality of sets of one or more target signature snippets and which each identify each genetic target of the group of genetic targets;
• receive and analyze in real time a plurality of portions of a test sequence output by a sequencer sequencing a sample, wherein each of the particular portions are analyzed within milliseconds of being sequenced by the sequencer and the sequencer outputs the particular portions of the test sequence at a rate of at least 4 megabytes per minute;
• determine in real time or near-real time with the output of the sequencer sequencing the sample before the sequencer has finished sequencing the sample and at a rate that is equal to or greater than the rate at which the sequencer outputs the particular portions of the test sequence, whether at least one universal target signature snippet of the set of one or more universal target signature snippets is present in at least one portion of the test sequence of the plurality of portions of the test sequence by comparing the test sequence to each of the one or more universal target signature snippets;
• determine, by the one or more processors and for each genetic target of the group of genetic targets, a respective probability the respective genetic target is present in the sample based at least on the determination of whether at least one universal target signature snippet of the set of one or more universal target signature snippets is present in the at least one portion of the test sequence of the plurality of portions of the test sequence;
• and
• output an analysis of the sample, the analysis indicating the respective probability that each genetic target is present in the sample.

A non-transitory computer-readable medium storing thereon sequences of computer-executable instructions for analyzing an output of a sequencer in real time, the sequences of computer-executable instructions including instructions that instruct at least one processor to to:

• identify a group of genetic targets, each genetic target being a target organism to be detected in a sample;
• determine a plurality of sets of one or more target signature snippets responsive to identifying the group of genetic targets, each set of one or more target signature snippet being derived from a genetic sequence of a respective genetic target of the group of genetic targets, wherein each of the plurality of sets of one or more target signature snippets (i) having previously been classified as corresponding to a respective genetic target of the group of genetic targets, (ii) 1 being derived from a genetic sequence of the respective genetic target, and (iii) do not correspond to snippets derived from a plurality of non-target organism sequences;
• filter the plurality of sets of one or more target signature snippets to identify a set of one or more universal target signature snippets, wherein the set of one or more universal target signature snippets consist of one or more target signature snippets that belong to each of the plurality of sets of one or more target signature snippets and which each identify each genetic target of the group of genetic targets;
• receive and analyze in real time a plurality of portions of a test sequence output by a sequencer sequencing a sample, wherein each of the particular portions are analyzed within milliseconds of being sequenced by the sequencer and the sequencer outputs the particular portions of the test sequence at a rate of at least 4 megabytes per minute;
• determine in real time or near-real time with the output of the sequencer sequencing the sample before the sequencer has finished sequencing the sample and at a rate that is equal to or greater than the rate at which the sequencer outputs the particular portions of the test sequence, whether at least one universal target signature snippet of the set of one or more universal target signature snippets is present in at least one portion of the test sequence of the plurality of portions of the test sequence by comparing the test sequence to each of the one or more universal target signature snippets;
• determine, by the one or more processors and for each genetic target of the group of genetic targets, a respective probability the respective genetic target is present in the sample based at least on the determination of whether at least one universal target signature snippet of the set of one or more universal target signature snippets is present in the at least one portion of the test sequence of the plurality of portions of the test sequence;
• and
• output an analysis of the sample, the analysis indicating the respective probability that each genetic target is present in the sample.