Tutorial
Basic settings
The pipeline is designed to run with a minimum of two supplied parameters:
* path to FASTQ sequence data (-s)
* path to reference database (-r)
The following command will run the pipeline on the supplied sequences with default parameters
assembly_pipeline.py -s /path/to/sequences -r /path/to/database
Optional parameters
There are a number of optional parameters than can be supplied to the assembly_pipeline.py script
-h, --help
show help message and exit
-v, --version
show program's version number and exit
-n, --numreads NUMREADS
Specify the number of reads. Paired-reads: 2,
unpaired-reads: 1. Default is paired-end
-t, --threads THREADS
Number of threads. Default is the number of cores in
the system
-c, --customsamplesheet CUSTOMSAMPLESHEET
Path of folder containing a custom sample sheet and
name of sample sheet file e.g.
/home/name/folder/BackupSampleSheet.csv. Note that
this sheet must still have the same format of Illumina
SampleSheet.csv files
-b, --basicassembly
Performs a basic de novo assembly, and does not
collect run metadata
-p, --preprocess
Performs quality trimming and error correction only. Do
not assemble the trimmed + corrected reads