Emil Haegglund
Appliction for scaffolding bacterial genomes in Real-time with SSPACE-longreads and MinION sequencing.

python (>=2.7, <3.0) Bokeh 0.11.0
Poretools 0.5.1
Watchdog
pyfasta

SSPACE-longreads

Download and install SSPACE-longreads from here.
Download the zip-file or use git to clone the repository. Install using python setup.py install.

Example run
schavott --sspace_path path_to_sspace --watch pass_download_dir_for_metrichor --contig_file path_to_contig_file --genome_size expected_genome_size

-h, --help
show this help message and exit

--scaffolder {links,sspace}, -s {links,sspace}
Which scaffolder to use. Only SSPACE-Longreads supported. (Default: SSPACE-Longreads)

--sspace_path SSPACE_PATH, -p SSPACE_PATH
Path to SSPACE

--watch WATCH, -w WATCH
Directory to watch for fast5 files

--contig_file CONTIG_FILE, -c CONTIG_FILE
Path to contig file

--run_mode {time,reads}, -r {time,reads}
Use timer or read count. (Default: reads)

--intensity INTENSITY, -i INTENSITY
How often the scaffolding process should run. If run mode is set to reads, scaffolding will run every i:th read. If run mode is time, scaffolding will run every i:th second. (Defaut: 100)

--stop STOP, -q STOP
Stop MinION when this number of scaffolds has been reached. (Not supported)

--genome_size GENOME_SIZE, -g GENOME_SIZ
Stop MinION when a scaffold is within 10 of this value. (Not supported)

--output OUTPUT, -o OUTPUT
Set output filename. (Defaut: schavott)