Method for assembling chloroplast genome sequence

Abstract

The invention discloses a method for assembling a chloroplast genome sequence. According to the method, the chloroplast does not need to be separated specially; a sample is sequenced by use of a new generation sequencing technique; Reads available in mapping into a reference genome are selected according to a reference chloroplast genome sequence; the Reads obtained by screening are assembled with a plurality of kmers to construct Contigs; the sequence of the Contigs and the reference chloroplast genome sequence are compared and ranked; the assembly and ranking result of one kmer is selected as the principal result, the extension of the sequence is realized according to the ranking result; the overlay regions of the polymerous sequences at the head and the tail are combined to obtain the complete sequence of the reference assembled chloroplast genome. The method for assembling the chloroplast genome sequence has the advantages that DeNovo assembly is performed by directly utilizing NGS genome sequencing data to obtain the complete chloroplast genome sequence, effective self-assembly and verified closed loop are realized, and the quality of the assembled sequence can be evaluated and determined.

Description

technical field [0001] The invention belongs to the technical field of biological information, and in particular relates to a method for assembling a chloroplast genome sequence. Background technique [0002] NGS Genome Sequencing (Next Generation Sequencing) is a next-generation DNA sequencing method with higher throughput and efficiency than traditional Sanger Sequencing. Roche's GS FLX sequencing system, ABI's (Applied Biosystems) SOLiD sequencing platform, and Illumina's Solexa sequencing platform are currently the world's leading NGS sequencing platforms. Compared with traditional Sanger sequencing, they all have higher throughput. , but each has different advantages and disadvantages. GS FLX sequencing has obvious advantages in read length. When the read length exceeds 400 bases, its accuracy can still reach more than 99%. However, the disadvantages of cost and throughput have limited its competition in NGS. The biggest advantage of SOLiD is High accuracy, the accura...

AI Technical Summary

Problems solved by technology

Although a lot of research has been carried out by many top scientific research institutions and personnel, a lot of progress has been made in accurately assembling large fragments from a large number of sequenced small fragments, but it is still extremely difficult to assemble a large complete genome, especially the nuclear genome. more difficult

[0004] The genomes of mitochondria and chloroplasts are relatively small. If pure mitochondria and chloroplasts are isolated and subjected to NGS sequencing, a complete genome sequence can generally be assembled at present, but the equipment requirements for separation and purification are high, difficult, and time-consuming.