Method and device for assembling genome sequence

Abstract

The invention discloses a method and device for assembling a genome sequence. The method comprises the following steps: filtering short segment sequences output after long insertion segment library tail end sequencing, thereby removing unqualified sequences; comparing the short segment sequences after filtering with a reference genome sequence; dividing paired short segment sequences for comparison into soap reads sequences, single reads sequences and unmap reads sequences according to the comparison result, and making statistics on the quantity of each type of sequences; calculating the distance between the paired short segment sequences on the same segment of the reference genome sequence by utilizing the soap reads sequences, and making statistics on the distance distribution of all the paired short segment sequences on the reference genome sequence; and when the distance distribution satisfies the threshold requirement, assembling the genome sequence by utilizing the unique paired single reads sequences with different segments on the reference genome sequence.

Description

technical field [0001] The present invention relates to the technical field of biological information, in particular, to a method and device for assembling genome sequences. Background technique [0002] With the birth of next-generation sequencing technologies 454 (Roche), Solexa (Illumina) and SOLiD (ABI), the sequencing throughput has increased rapidly while the cost of sequencing has dropped sharply. This breakthrough in next-generation sequencing technology has greatly promoted the development of genome science, and the whole genome sequences of a large number of species have been published, including James Watson's personal genome, the genome of the first Asian, giant panda, cucumber, etc. [0003] Each round of sequencing of the next-generation sequencer can obtain millions of short-segment sequences, and several rounds of such sequencing are required to completely sequence a genome, which means that in order to obtain a complete genome Atlases must map, localize, an...

AI Technical Summary

Problems solved by technology

In the prior art, since the fragment sequences generated during sequencing are very short, it takes a very large amount of calculation to complete the restoration of large fragment data

[0005] At the same time, as one of the measures of the quality of the genome map, the fragment length N50 (N50 is to arrange all the assembled sequences from large to small and add them according to the length, when the length obtained by adding is 100% of the total length of all assembled sequences The length of the assembly sequence at 50% can refer to Miller et al.2010.Assembly algorithms for next generation sequencing data.Genomics.95(6):315-327) The index is also affected by the library that can be constructed in the experiment Insert length limitations have been a significant bottleneck

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