TRANSCRIPTOME ASSEMBLY METHOD AND SYSTEM

摘要

Provided is a transcriptome assembly method, comprising the following steps of: constructing a sequencing sample transcriptome read into a de Brujin graph; performing filtering and linearization processing on the de Brujin graph, so as to form continuous contigs; obtaining association among the contigs, and filtering association data; performing linearization processing on a continuous sequence without bifurcation; outputting a contig sequence; comparing the read and an end pairing read with the output contig sequence, so as to obtain information between the read and the contig; establishing connections among the contigs, so as to construct a graph with the contigs as points and the connections as edges; pre-processing and dividing the obtained graph, so as to obtain independent sub-graphs; and outputting a transcript according to the sub-graphs. Further provided is a transcriptome assembly system based on the method.

主权项

1. A method for contig assembly, comprising following steps:
(1) constructing a de Brujin graph based on transcriptomic reads obtained from a sample; (2) subjecting the de Brujin graph obtained in the step (1) to a first filtration and a first linearization, to form continuous contigs; (3) obtaining a connection relationship among the contigs, and subjecting the connection relationship to a second filtration; (4) subjecting continuous contigs without a fork to a second linearization; (5) repeating step the (3) and the step (4) until a sequence presents no changes, to obtain the sequence assembling with contigs.