A list of software for Oxford Nanopore data
- Robocopy.exe (Windows)
- Installed on all Windows machines
- File synchronisation tool run from within the cmd.exe command prompt
C:\Users\Mick> C:\Windows\System32\robocopy.exe C:\data\reads Z:\path\to\my\network\share /MIR /FFT /Z /XA:H /W:5
- rsync (Windows)
- Can be (optionally) installed with Cygwin
- run from within the cmd.exe command prompt or Cygwin Terminal
rsync -avP C:/data/reads mwatson9@myserver.ac.uk:/path/to/my/data
- rsync (Windows 10)
- It is possible to install an entire Ubuntu sub-system on Windows 10
- C:\ drive is accessible within bash from /mnt/c/
rsync -avP /mnt/c/data/reads/ mwatson9@myserver.ac.uk:/path/to/my/data
- rsync (Linux or Mac)
- Terminal/shell available on both
rsync -avP /path/to/fast5/ mwatson9@myserver.ac.uk:/path/to/my/data
- Albacore
- Available from the Oxford Nanopore community
# run with -l to figure out which model to use
read_fast5_basecaller.py -l
# run the basecaller
read_fast5_basecaller.py -i /vol/raw_fast5/ \
-r \
-t 4 \
-s output_dir \
-o fastq,fast5 \
-c r94_450bps_linear.cfg \
--barcoding
- poretools
- poRe
- NanoOK
- bwa mem
- LAST
- GraphMap
- MiniMap2
- NGMLR
- Nanopolish
- SPAdes
- Minimap / miniasm
- Canu
- Nanopolish
- SSPACE-LongReads
- LINKS
- Sniffles