Compression storage and construction method of bidirectional multi-step debruijn graph
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A compression storage, two-way multi-step technology, applied in special data processing applications, instruments, electrical digital data processing, etc., to achieve the effect of improving the speed of splicing and reducing the memory consumption of a single machine
Active Publication Date: 2016-01-27
SHENZHEN INST OF ADVANCED TECH
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Problems solved by technology
[0007] The technical problem to be solved by the present invention is to improve the running speed of sequence splicing in the prior art and reduce the memory consumption of a single machine
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Embodiment 1
[0058] A method for compressing, storing and constructing a bidirectional multi-step deBruijn graph provided by an embodiment of the present invention includes the following steps:
[0059] Compression storage steps, specifically
[0060] S11. Read a sequence s;
[0061] S12. Cut the sequence s into multiple segments t using a sliding window of length k; wherein 0
[0062] S13. For each fragment t, use the nucleic acid encoding table {A:00, C:01, G:10, T:11} to encode, and represent it as a 64-bit integer a;
[0063] S14. Reverse the string of the segment t, and use the symmetric complementation table {A->T, C->G, G->C, T->A} to change each character in the reversed string to its Complementary characters, obtain a string v of complementary characters, and use the nucleic acid encoding table in step S13 again to encode the string v, and represent it as a 64-bit integer b;
[0064] S15, take the maximum number of integer a and integer b as the sig...
Embodiment 2
[0078] Another embodiment of the present invention provides a method for compressing, storing and constructing a bidirectional multi-step deBruijn graph, comprising:
[0079] Compression storage steps, specifically
[0080] S11. Read a sequence s;
[0081] S12. Cut the sequence s into multiple segments t using a sliding window of length k; wherein 0
[0082] S13. For each fragment t, use the nucleic acid encoding table {A:00, C:01, G:10, T:11} to encode, and represent it as a 64-bit integer a;
[0083] S14. Invert the fragment t, use the symmetric complementation table to complement the inverted fragment to obtain a complementary fragment, and use the nucleic acid encoding table in step S13 again to encode the complementary fragment and express it as a 64-bit integer b ;
[0084] S15, take the maximum number of integer a and integer b as the sign number of k molecules of fragment t and complementary fragment v;
[0085] S16. Repeat steps S11-S1...
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Abstract
The invention relates to a compressed storage and construction method of a two-way multi-step de Bruijn graph, and the compressed storage and construction method of the two-way multi-step de Bruijn graph includes compressed storage steps and de Bruijn graph construction steps. The compressed storage and construction method of the two-way multi-step de Bruijn graph includes the steps of (1) carrying out a structure optimization for the de Bruijn graph by combining with the characteristics of the deoxyribonucleic acid (DNA) order complementary double-helix structure, and halving nodes of the graph to be stored by using two-way multi-step de Bruijn graph, (2) using a compressed storage technology of the two-way multi-step de Bruijn graph to enable memory consumption of storing the two-way multi-step de Bruijn graph to be controlled within 100 times size of a reference sequence so that the problem that the sequence-assembled original de Bruijn graph scale is enormous unusually so as to bring a storage pressure to the memory consumption can be solved, and (3) constructing two-way multi-step de Bruijn graph, the DNA sequence assembling problem being capable of being decomposed into the edge fusant problem, and suitable for parallel computing.
Description
【Technical field】 [0001] The invention relates to the field of gene sequencing, in particular to a compression storage and construction method of a bidirectional multi-step deBruijn graph. 【Background technique】 [0002] The sequence fragments generated by next-generation gene sequencing technology have the characteristics of short sequence, high coverage, additional double-ended information, etc., which make the original traditional sequence splicing technology unusable, and increase the complexity and difficulty of sequence splicing technology. In the face of massive data, efficient sequence splicing technology has become the key to processing sequencing data. [0003] The technical problem of sequence splicing is mainly transformed into the knowledge of graph theory to solve. At present, there are two main ways to solve the problem of sequence splicing technology. One way is the traditional overlap-then-expansion method, that is, the OLC (Overlap-Layout-Consensus) metho...
Claims
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