Method and apparatus for detecting pathogens

A real-time method for detecting a pathogen in a sample, the method comprising:

• inputting a plurality of sequence reads which are obtained from the sample using nucleic acid sequencing;
• and
• for each input sequence read in the plurality of sequence reads:
• comparing, using a first classification algorithm, the input sequence read to a plurality of target sequences in a first database, wherein the first database comprises nucleic acid sequences for pathogens;
• identifying, using the first classification algorithm, a set of hits for the input sequence read, wherein each hit is a target sequence which matches the input sequence read;
• assigning, using the set of hits, the input sequence read to a taxon;
• and
• classifying the input sequence read as potentially pathogenic when the taxon to which the input sequence read is assigned corresponds to a pathogen taxon;
• and
• when the input sequence read is classified as potentially pathogenic:
• comparing, using a second classification algorithm, the potentially pathogenic input sequence read to a plurality of target sequences in a second database, wherein the second database is selected based on the pathogen taxon which corresponds to the taxon to which the input sequence read is assigned;
• and
• confirming the classification of the potentially pathogenic input sequence read as pathogenic when the potentially pathogenic input sequence read matches one or more target sequences in the second database;
• wherein the method further comprises
• calculating a confidence score for each input sequence read by incrementing the confidence score by a first fixed amount when the input sequence read is classified as potentially pathogenic and by incrementing the confidence score by a second fixed amount when each input sequence read which is classified as potentially pathogenic is confirmed to be pathogenic, and
• comparing the confidence score to a confidence score threshold to determine whether each input sequence read is a match to a pathogen.