Paired-Reads-Assemble

you should assemble two types of reads using the De Bruijn graph representation and the Eulerian path to obtain the original sequence from that representation.

Pair-reads with a known distance between them

Input : Your program should be able to read a file. The first line would be: - the length of the sequences in each side and the length of the gap. - Each read will take one. - The pair reads will be separated by “|” .. Example : AGCC|TTAA Output : The program then outputs the assembled sequence to the screen.

Explain

READS

GACC|GCGC

ACCG|CGCC

CCGA|GCCG

CGAG|CCGG

GAGC|CGGA

GRAPH

(S)GAC,GCG --> ACC,CGC

ACC,CGC --> CCG,GCC

CCG,GCC --> CGA,CGC

CGA,CCG --> GAG,CGG

GAG,CGG --> AGC,GGA(E)

PATHS use the first letter only in all expect the last one get all its letters

GAC -> ACC -> CCG -> CGA -> GAG -> AGC

Prefix = GACCGAGC

GCG -> CGC -> GCC -> CCG -> CGG -> GGA

suffix = GCGCCGGA

the final result should be like

Genome = GACCGAGCGCCGGA