/Gene-Assembing-Program

A program which can assembing .fasta file generated by Next Generation Sequencing(NGS) de novo using De Bruijn Graph Algorithm, and can also choose to map(BLAST) the contigs to a reference sequence

Primary LanguageJava

Gene Assembing Program for NGS

Overview

This is a program which can assembing gene fragments from Next Generation Sequencing(NGS) de novo.

It implements two main functions:

-Assembling gene contigs from gene fragments in .fasta file from NGS de novo using De Bruijn Algorithms.

-Provide a user optional function mapping contigs to reference sequence using heuristic algorithms like BLAST.

The k-mer data is stored in a self-defined hash table to optimize storage space and reduce computional complexity.

Specification

GUI of this program is in Chinese, and a specification in English is shown below.

Specification