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Shannon Version 0.0.0
###Usage
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.
###Options
The string [options] can be either empty or one or more of the following:
-p nJobs
This option is used in order to specify the number of parallel jobs. Needs GNU parallel installed.
-K kmerSize
This option is used to set the Kmer size.
--partition partitionSize
This option is used to set the maximum size of each partition.
--compare reference_file_name
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.
###Output
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.