ont_sig_align

Nanopore signal aligner

Installation

Prerequisites:

-Fast5:

cd src
git clone https://github.com/mateidavid/fast5
make

• HDF5: Should be included on the MARCC server at location specified in Makefile. Otherwise:

cd src
wget https://support.hdfgroup.org/ftp/HDF5/current18/bin/linux-centos7-x86_64-gcc485/hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz
tar -xzvf hdf5-1.8.18-linux-centos7-x86_64-gcc485-shared.tar.gz

• Boost: Should be included on the MARCC server at location specified in Makefile. Otherwise:

# make sure boost is installed
sudo apt-get install libboost1.58-all-dev
# find where the boost libraries are located on your computer, set to $BOOSTDIR
cd src
bcp --boost=$BOOSTDIR math/distributions boost/

Compilation

make sure BOOST_INCLUDE, HDF5_INCLUDE and HDF5_LIB are set accordingly in Makefile

make

running

./sigalign REFERENCE.FASTA MODEL TALLY_DISTANCE READ1.FAST5 READ2.FAST5 ...

expected output:

READ1.FAST5: <x> matches on fwd strand, <y> matches on rev strand
READ2.FAST5: <x> matches on fwd strand, <y> matches on rev strand