Systems And Methods For Transmission And Pre-Processing Of Sequencing Data

Abstract

“Omic” digital data transport systems and methods are disclosed. The disclosed systems and methods employ a transport server that assembles a transport group larger numbers of omic output files on the basis of machine specific annotation from one or more sequencing devices and user input related to one or more attributes for the omic output files.

What is claimed is: 
     
         1 . A method of transferring a plurality of omic sequences, comprising:
 providing an access to a first computer coupled with a second computer;   receiving, by the first computer, a plurality of omic output files from a plurality of respective sequencers, wherein each of the omic output files comprises sequence data and a machine-specific annotation;   annotating, by the first computer, the plurality of omic output files using an annotation input from a user to thereby form annotated omic output files;   grouping, by the first computer, the annotated omic output files into a transport group, wherein grouping is based on the machine-specific annotation and the annotation input from the user;   delivering, by the first computer, the transport group to the second computer; and,   sending, by the first computer or the second computer, a feedback signal to the second computer or the first computer, respectively, to modify an operation of at least one of the first computer, the second computer, and the sequencer.   
     
     
         2 . The method of  claim 1 , wherein the omic output files are genomic output files, RNA-omic output files, or proteomic output files. 
     
     
         3 . The method of  claim 1 , wherein the operation comprises converting the plurality of omic output files from a raw format into a SAM format or a BAM format. 
     
     
         4 . The method of  claim 1 , wherein the operation comprises temporarily storing the plurality of omic output files in a memory prior to the step of receiving the plurality of omic output files by the first computer. 
     
     
         5 . The method of  claim 1 , wherein the operation comprises changing an operational parameter or going offline of the sequencer. 
     
     
         6 . The method of  claim 1 , wherein the operation comprises delivering additional omic data. 
     
     
         7 . The method of  claim 1 , wherein the operation comprises stopping delivery of the transport group from the first computer. 
     
     
         8 . The method of  claim 1 , wherein the operation comprises repeating a particular omic analysis in the sequencer. 
     
     
         9 . The method of  claim 1 , wherein the operation comprises sending a signal from the second computer indicating presence or absence of particular data. 
     
     
         10 . The method of  claim 1 , wherein the at least one of the plurality of sequencers receive another feedback signal from the first computer or the second computer. 
     
     
         11 . The method of  claim 1 , wherein the at least one of the plurality of sequencers receive another feedback signal from the first computer and the second computer. 
     
     
         12 . The method of  claim 1 , wherein the machine-specific annotation comprises an annotation selected from the group consisting of a date and/or time identifier, a sequencing device identifier, a lane identifier, a quality score, and a pair member identifier. 
     
     
         13 . The method of  claim 1 , wherein the annotation input from the user comprises an annotation selected from the group consisting of an analysis type annotation and a patient specific annotation. 
     
     
         14 . The method of  claim 11 , wherein the analysis type annotation is selected from the group consisting of a whole genome analysis, exome enrichment analysis, transcriptome analysis, and proteome analysis. 
     
     
         15 . The method of  claim 1 , wherein the step of grouping is performed in real time. 
     
     
         16 . The method of  claim 1 , wherein the step of delivering the transport group is performed upon completion of forming the transport group. 
     
     
         17 . The method of  claim 1 , wherein the step of grouping is performed independently of actual sequence content.