Method and system for selective access of stored or transmitted bioinformatics data

Abstract

The storage or transmission of genomic data is realized by employing a structured compressed genomic dataset in a file or in a stream of genomic data. Selective access to the data, or subsets of the data, corresponding to specific genomic regions is achieved by employing user-defined labels based on data classification and a specific indexing mechanism.

1 . A method for selective access of regions of genomic data by employing labels, said labels comprising: an identifier of a reference genomic sequence, an identifier of said genomic regions, and an identifier of the data class of said genomic data,
 wherein said genomic data are sequences of genomic reads, and   wherein said data classes can be of the following type or a subset of them:
 “Class P” comprising genomic reads which do not present any mismatch with respect to a reference sequence, 
 “Class N” comprising genomic reads including only mismatches in positions where the sequencing machine was not able to call any “base” and the number of said mismatches does not exceed a given threshold, 
 “Class M” comprising genomic reads in which mismatches are constituted by positions where the sequencing machine was not able to call any base, named “n type” mismatches, and/or it called a different base than the reference sequence, named “s type” mismatches, and said numbers of mismatches do not exceed given thresholds for the number of mismatches of “n type”, of “s type” and a threshold obtained from a given function (f(n,s)), 
 “Class I” when the genomic reads can possibly have the same type of mismatches of “Class M”, and in addition at least one mismatch of type: “insertion” (“i type”), “deletion” (“d type”), soft clips (“c type”), and wherein the numbers of mismatches for each type does not exceed the corresponding given thresholds and a threshold provided by a given function (w(n,s,i,d,c)), 
 “Class U” comprising all reads that do not find any classification in the classes P, N, M, I. 
   
     
     
         2 . (canceled) 
     
     
         3 . (canceled) 
     
     
         4 . The method of  claim 1 , further comprising the case of said genomic data being paired sequences of genomic reads. 
     
     
         5 . The method of  claim 4  wherein said data class of paired reads can be of the following types or a subset of them:
 “Class P” comprising genomic read pairs which do not present any mismatch with respect to a reference sequence, 
 “Class N” comprising genomic reads pairs including only mismatches in positions where the sequencing machine was not able to call any “base” and said numbers of mismatches for each read do not exceed a given threshold, 
 “Class M” comprising genomic read pairs including only mismatches in positions where the sequencing machine was not able to call any “base” and said numbers of mismatches for each read do not exceed a given threshold, named “n type” mismatches, and/or it called a different base than the reference sequence, named “s type” mismatches, and said numbers of mismatches does not exceed a given thresholds for the number of mismatches of “n type”, of “s type” and a threshold obtained from a given function (f(n,s)), 
 “Class I” comprising read pairs which can possibly have the same type of mismatches of “Class M” pairs, and in addition at least one mismatch of type: “insertion” (“i type”) “deletion” (“d type”) soft clips (“c type”), and wherein the number of mismatches for each type does not exceed the corresponding given threshold and a threshold provided by a given function (w(n,s,i,d,c)), 
 “Class HM” comprising read pairs for which only one read mate does not satisfy the matching rules for being classified in any of the classes P, N, M, I, 
 Class “U” comprising all reads pairs for which both reads do not satisfy the matching rules for being classified in the classes P, N, M, I. 
 
     
     
         6 . The method of  claim 1 , wherein said identifier of said genomic regions is comprised in a master index table. 
     
     
         7 . The method of  claim 6  wherein said genomic data and said labels are entropy coded. 
     
     
         8 . The method of  claim 7  wherein said master index table is comprised in a genomic dataset header. 
     
     
         9 . The method of  claim 8 , wherein said regions of genomic data are dispersed among separate Access Units. 
     
     
         10 . The method of  claim 9  wherein the location of said regions of genomic data, in a file, is indicated in a local index table. 
     
     
         11 . The method of  claim 1 , wherein said labels are user specified. 
     
     
         12 . The method of  claim 1 , wherein said regions are protected and/or encrypted in a separate manner, without encrypting the whole genomic file. 
     
     
         13 . The method of  claim 1 , wherein said labels are stored in a genomic label list (GLL). 
     
     
         14 . A method for encoding genomic data with selective access to regions of genomic data as claimed in  claim 1 . 
     
     
         15 . The method of  claim 13 , wherein said genomic label list is periodically retransmitted or updated in order to enable multiple synchronization points. 
     
     
         16 . A method for decoding a stream or a file of genomic data with selective access to regions of genomic data as claimed in  claim 1 . 
     
     
         17 . An apparatus for encoding genomic data as claimed in  claim 14 . 
     
     
         18 . An apparatus for decoding genomic data as claimed in  claim 16 . 
     
     
         19 . Storing means for storing genomic data encoded according to  claim 14 . 
     
     
         20 . A computer-readable medium comprising instructions that when executed cause at least one processor to perform the encoding method of  claim 14 . 
     
     
         21 . A computer-readable medium comprising instructions that when executed cause at least one processor to perform the decoding method of  claim 16 .