Getting Started
The short tutorial below explains how to run Shannon using a small example distributed with the program.
The program includes some short read files to test if the program is running properly.
We will assemble Samples/SE_read.fasta first:
python shannon.py -o ../ShannonOutput --single Samples/SE_read.fasta
Similarly we can assemble a fastq file now:
python shannon.py -o ../ShannonOutput --single Samples/SE_reads.fastq
We can also assemble paired-end reads as follows:
python shannon.py -o ../ShannonOutput --left Samples/PE_read_1.fastq --right Samples/PE_read_2.fastq