Shannon Version 0.0.0
For single-ended reads,
Usage: python shannon.py -o running_directory --single read_file [options]
For paired-end reads,
Usage: python shannon.py -o running_directory --left read_pair1 --right read_pair2 [options]
The running_directory mentions the name of a directory where Shannon can run. This directory should be empty or non-existent while starting the run.
The reads should be in fasta or fastq format.
The string [options] can be either empty or one or more of the following:
This option is used in order to specify the number of parallel jobs. Needs GNU parallel installed.
This option is used to set the Kmer size.
This option is used to set the maximum size of each partition.
This option is used to compare the produced output to the reference and create a log. To run this option blat has to be installed.
The main output is in running_directory/shannon.fasta which contains the list of reconstructed transcripts in fasta format.
There is a log file in running_directory/log.txt
The output of the –compare option is in running_directory/compare_log.txt
The directory running_directory/TEMP contains intermediate running files and can be deleted after the run.
~~~ ### Requirements
Memory: Please reserve atleast 1GB / 1 million single-end reads.
Cores: The program is partially multi-threaded and needs GNU parallel to run.
Disk Space: The program will use upto 5 times the amount of space required for storing the reads (in FASTA format). Please ensure you have this amount of space before running.