deBruijn graph based assembly is the most easy way to assemble an NGS library. In this, the sequence can be represted in terms of its k-mer components. Users are reuested to check http://www.homolog.us/Tutorials/index.php?p=2.1&s=1 for a basic idea of how k-mer based assembly is done.
This script is helpful in assembling the sequence based on its k-mers. ######NOTE As of now the script only handles the k-mers with no repetition.
Example of k-mer file:
TGGAAGT
GGAAGTC
GAAGTCG
AAGTCGC
AGTCGCG
GTCGCGG
TCGCGGA
CGCGGAA
GCGGAAT
CGGAATC
USAGE: perl debruijn.pl kmer_file.txt
Assembled sequence:
ATGGAAGTCGCGGAATC
As a default, overlaps were checked with 6 residues of each k-mer(7-mer). Users can modify the script according
to their needs by changing the length in substr function (line 20 in the script).