Project : Genome assembly

Author : Gautier COUTURE

Pre-requisites

Requires Biopyhton to function correctly :

$ pip install Biopython

Usage :

• Windows :

  $ py Assembly.py -h

• Linux :

  $ python3 Assembly.py -h

Program Settings :

-h, --help show this help message and exit
-d , --dataset Path to a fasta file that contain reads to assemble
-e , --errors Indicates whether the given dataset contain sequencing errors or not (0: No, 1: Yes)
-o , --out Output file name (& path)
-k , --kmersize Size of kmers we need (Optional, Default : 10)

Exemple:

$ python3 Assembly.py -d DatasetAssembly/Sequencage1.fa -e 1 -o output.fa -k 25

Implemented features :

• K-mer Index
• Reconstruction of the reference using sequencing data without errors
• K-mer filter (Low occurences)

Unfinished features :

• Graph cleaning

Non Implemented features :

• Reconstruction of the reference using sequencing data with errors