An optimised re-implementation of the call-methylation module in Nanopolish. Given a set of basecalled Nanopore reads and the raw signals, f5c detects the methylated cytosine bases. f5c can optionally utilise NVIDIA graphics cards for acceleration.
First the reads have to be indexed using
f5c index (or
nanopolish index - f5c index is the same code as nanopolish index). Then invoke
f5c call-methylation to detect methylated cytosine bases. The result is almost the same as from nanopolish except a few differences due to floating point approximations.
If you are a Linux user and want to quickly try out download the compiled binaries from the latest release. For example:
VERSION=v0.1-beta wget "https://github.com/hasindu2008/f5c/releases/download/$VERSION/f5c-$VERSION-binaries.tar.gz" && tar xvf f5c-$VERSION-binaries.tar.gz && cd f5c-$VERSION/ ./f5c_x86_64_linux # CPU version ./f5c_x86_64_linux_cuda # cuda supported version
Binaries should work on most Linux distributions and the only dependency is
zlib which is available by default on most distros.
Users are recommended to build from the latest release tar ball. You need a compiler that supports C++11. Quick example for Ubuntu :
sudo apt-get install libhdf5-dev zlib1g-dev #install HDF5 and zlib development libraries VERSION=v0.1-beta wget "https://github.com/hasindu2008/f5c/releases/download/$VERSION/f5c-$VERSION-release.tar.gz" && tar xvf f5c-$VERSION-release.tar.gz && cd f5c-$VERSION/ scripts/install-hts.sh # download and compile the htslib ./configure make # make cuda=1 to enable CUDA support
The commands to install hdf5 (and zlib) development libraries on some popular distributions :
On Debian/Ubuntu : sudo apt-get install libhdf5-dev zlib1g-dev On Fedora/CentOS : sudo dnf/yum install hdf5-devel zlib-devel On Arch Linux: sudo pacman -S hdf5 On OS X : brew install hdf5
If you skip
./configure hdf5 will be compiled locally. It is a good option if you cannot install hdf5 library system wide. However, building hdf5 takes ages.
Building from the Github repository additionally requires
autoreconf which can be installed on Ubuntu using
sudo apt-get install autoconf automake.
NVIDIA CUDA support
To build for the GPU, you need to have the CUDA toolkit installed. Make nvcc (NVIDIA C Compiler) is in your PATH.
The building instructions are the same as above except that you should call make as :
Optionally you can provide the CUDA architecture as :
make cuda=1 CUDA_ARCH=-arch=sm_xy
If your CUDA library is not in the default location /usr/local/cuda/lib64, point to the correct location as:
make cuda=1 CUDA_LIB=/path/to/cuda/library/
Visit here for troubleshooting CUDA related problems.
f5c index -d [fast5_folder] [read.fastq|fasta] f5c call-methylation -b [reads.sorted.bam] -g [ref.fa] -r [reads.fastq|fasta]
Visit the man page for all the commands and options.
Follow the same steps as in Nanopolish tutorial while replacing
f5c. If you only want to perform a quick test of f5c :
#download and extract the dataset including sorted alignments wget -O f5c_na12878_test.tgz "http://genome.cse.unsw.edu.au/tmp/f5c_na12878_test.tgz" tar xf f5c_na12878_test.tgz #index and call methylation f5c index -d chr22_meth_example/fast5_files chr22_meth_example/reads.fastq f5c call-methylation -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv