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  -o ../ShannonOutput --single Samples/SE_read.fasta

Similarly we can assemble a fastq file now:

python -o ../ShannonOutput --single Samples/SE_reads.fastq 

We can also assemble paired-end reads as follows:

python -o ../ShannonOutput --left Samples/PE_read_1.fastq --right Samples/PE_read_2.fastq