https://github.com/jts/nanopolish
nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more
Dependencies
A compiler that supports C++11 is needed to build nanopolish. Development of the code is performed using gcc-4.8.
By default, nanopolish will download and compile all of its required dependencies. Some users however may want to use system-wide versions of the libraries. To turn off the automatic installation of dependencies set HDF5=noinstall, EIGEN=noinstall, HTS=noinstall or MINIMAP2=noinstall parameters when running make as appropriate. The current versions and compile options for the dependencies are:
- libhdf5-1.8.14 compiled with multi-threading support
--enable-threadsafe - eigen-3.2.5
- htslib-1.4
- minimap2-d2de282
In order to use the additional python3 scripts within /scripts, install the dependencies via
pip install -r scripts/requirements.txt --user
more requirements.txt
setuptools>=42.0.2
cython>=0.29.14
numpy>=1.18.0
scikit-learn>=0.22
h5py>=2.10.0
tqdm>=4.41.0
matplotlib>=3.0.3
seaborn>=0.9.0
biopython>=1.76
pysam>=0.15.3
pandas>=0.24.0
scipy>=1.3.0
WARNING: The scripts cygdb, cython and cythonize are installed in '/root/.local/bin' which is not on PATH.
Installation instructions
Installing the latest code from github (recommended)
You can download and compile the latest code from github as follows:
git clone --recursive https://github.com/jts/nanopolish.git
cd nanopolish
make /home/software/nanopolish/nanopolish/nanopolish
usage: nanopolish [command] [options]
valid commands:
--help
--version
call-methylation
eventalign
extract
getmodel
help
index
methyltrain
phase-reads
polya
scorereads
variants
vcf2fasta
for help on given command, type nanopolish command --help
The main subprograms of nanopolish are:
nanopolish call-methylation: predict genomic bases that may be methylated
nanopolish variants: detect SNPs and indels with respect to a reference genome
nanopolish variants --consensus: calculate an improved consensus sequence for a draft genome assembly
nanopolish eventalign: align signal-level events to k-mers of a reference genome