nanopore-software

A list of software for Oxford Nanopore data

Moving 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

Basecalling

• 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

QC

• minion_qc
  • code
• NanoFilt
  • blog
• PoreChop
  • PoreChop
  • code

Extract data from FAST5

• poretools
• poRe
• NanoOK

Mapping / Aligning

• bwa mem
• LAST
• GraphMap
• MiniMap2
• NGMLR

Variant Calling

• Nanopolish

Assembly

• SPAdes
• Minimap / miniasm
• Canu

Polishing

• Nanopolish

Scaffolding

• SSPACE-LongReads
• LINKS

Structural variants

• Sniffles

Pipelines