Schavott v0.4.1

Applictions to monitor scaffolding or assembly of bacterial genomes in Real-time with MinION sequencing.
SSPACE-longreads or links can be used for scaffolding, and the minimap/miniasm pipeline can be used for assembly.

Python-requirements

Python (>=2.7, <3.0)
Bokeh
h5py 2.2.0
Watchdog 0.8.3
pyfasta

Applications

SSPACE-longreads, links and/or minimap/miniasm

Instructions

Download and install SSPACE-longreads from here.
Download the zip-file or use git to clone the repository. Install using python setup.py install.
A bokeh server must be running on the computer for the application to start, this is used to plot the result in a web browser.

To start a bokeh server, run the following command in the terminal:
bokeh serve

Example run
SSPACE-longreads
schavott --scaffolder sspace_path path_to_sspace --watch pass_download_dir_for_metrichor --contig_file path_to_contig_file

links
schavott --scaffolder links --watch pass_download_dir_for_metrichor --contig_file path_to_contig_file

minimap/miniasm
schavott --run_mode assembly --min_read_length 5000 --min_quality 8 --watch pass_download_dir_for_metrichor

Arguments

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

--run_mode {scaffold, assembly}
Assemble or scaffold genome using MinION reads.

--scaffolder {SSPACE, links}
If scaffold, which scaffolder to use.

--sspace_path SSPACE_PATH, -p SSPACE_PATH
In case SSPACE is used, give the path to SSPACE.

--watch WATCH, -w WATCH
Directory to watch for fast5 files, usually metrichor downloads/pass folder.

--min_read_length
Minimum read length to use. (Default: 5000)

--min_quality
Minimum read quality. (Default: 9)

--skip SKIP, -j SKIP Skip the first reads of the sequencing run. (Default: 0)

--contig_file CONTIG_FILE, -c CONTIG_FILE
Path to contig file if scaffolding, fasta-format.

--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)

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

--plot
Show bokeh GUI in web-browser, this require a bokeh server to run.

Test run using old MinION data

It is possible to test the application using already sequenced data. To do this, the time-information and the path to the fast5-files must be extracted. To do this, run poretools times on the folder containing the fast5-files.

poretools times path/to/fast5-dir > times.csv

In a second terminal start the Schavott application using the previously described commands, and set the watch directory to target_dir. Next the move_fast5.py script is run to simulate the creation of new fast5-files in the target directory, files are copied from the fast5-files source directory to the target directory using the time information in the fast5-files.

python move_fast5.py times.csv target_dir/ real-time

If you want to speed things up when testing, you could always change real-time to fast-forwardor super-sonic.