Genome assembly algorithm inGAP-sf based on direct connection information.

In December 2016, the international academic journal Nucleic Acids Research published the latest research results of the Zhao Fangqing team of the Computational Genomics Laboratory of the Beijing Institute of Life Sciences of the Chinese Academy of Sciences entitled "The combinon of direct and paired link graphs can boost repetitive genome assembly" (click on the bottom left corner to read the original article).
The study built a direct connection infographic based on the overlap of the contig, and with the help of the pairing connection information, solved the problem of genome stitching fragmentation caused by the repeat sequence of the short segment, extended the length of the sequence under the premise of ensuring accuracy, and obtained a more complete and less interstitial genome sequence.
has long been a major constraint to genome stitching, and assembly of repeat sequence regions rich in short segments is a difficult hurdle to overcome.
this part of the sequence can lead to gene fractures, allowing certain key genetic information to be omitted from subsequent research analyses.
the previous sequence assembly algorithm only used pairing connection information, ignoring the connection relationship of the config itself, which not only made the algorithm more difficult, but also the stitching results also had many gap sequences, many false connections and so on.
especially for short segment repeat sequences, the traditional assembly algorithm has chosen to discard directly, so that the segment repeat sequence rich area can not be effectively stitched.
this situation, Zhao Fangqing's team developed inGAP-sf, a genomic assembly algorithm based on direct connection information.
This method builds a direct connection infographic based on the overlapping parts of thecontig, topology paths under the supervision of the paired connection information, and integrates these paths, and introduces the Bayes model to remove the wrong path, resulting in high-quality stitching results.
tests on multiple simulation data and real sequencing data, the results of inGAP-sf are greatly improved compared to the stitching sequence obtained by other methods.
the stitching strategy used in this study perfects the shortage of sequence assembly algorithm to a great extent, and provides a new way of thinking for sequence stitching.
inGAP-sf has been published for use by relevant researchers.
work was jointly completed by Shi Wenxuan and Yu Peifeng of Zhao Fangqing's task force, and was supported by funding from the National Natural Science Foundation of China and the Ministry of Science and Technology's key research and development programs.
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