Characterization of molecules in nanofluidics

A method of characterizing a sample comprising polynucleotide sequences, the method comprising:

• labeling a plurality of sample nucleic acid molecules, each of about 10 base pairs to about 500 base pairs, with at least a first label, wherein the sample nucleic acid molecules comprise polynucleotide sequences of a genome or a fragment or fragments thereof, wherein the polynucleotide sequences of the sample nucleic acid molecules are from the sample;
• providing a plurality of labeled control nucleic acid molecules, each of about 10 base pairs to about 500 base pairs, wherein the control nucleic acid molecules comprise polynucleotide sequences of the genome or fragment or fragments thereof;
• translocating the plurality of labeled sample nucleic acid molecules through one or more fluidic nanochannels having a length of at least 10 nm and a cross-sectional diameter of less than 1000 nm;
• translocating the labeled control nucleic acid molecules through one or more fluidic nanochannels having a length of at least 10 nm and a cross-sectional diameter of less than 1000 nm;
• detecting physical counts of signals from the labeled sample nucleic acid molecules, said signals comprising patterns characteristic of the genome or fragment or fragments thereof;
• detecting physical counts of signals from the labeled control nucleic acid molecules, said signals comprising patterns characteristic of the genome or fragment or fragments thereof;
• and
• aligning the patterns to a reference of the genome or fragment or fragments thereof, thereby ascertaining:
• a coverage depth for the sample nucleic acid molecules over the reference of the genome or fragment or fragments;
• and
• a coverage depth for the control nucleic acid molecules over the reference genome or fragment or fragments;
• and
• determining a copy number of the genome or fragment or fragments thereof in the sample.