Sigmap
Sigmap is a streaming method for mapping raw nanopore signal to reference genomes.
Installation
First get the repo with submodules (make sure you use --recursive):
git clone --recursive git@github.com:haowenz/sigmap.git
Make sure you have GCC version > 8. Then just run:
cd sigmap && make
Usage
First, an index needs to be built for the reference using ONT pore models (as a submodule in the extern folder). We use yeast genome as an example:
./sigmap -i -r yeast.fasta -p extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model -o yeast_index
It will generate the index file yeast_index.si. Note that a genome point cloud file yeast_index.pt will also be saved. But it can also be generated very quickly on the fly every time before mapping. After index construction, yeast raw signals in fast5 format or blow5 format can be mapped using
./sigmap -m -r yeast.fasta -p extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model -x yeast_index -s /path/to/yeast/fast5_or_blow5/dir -o yeast_mapping.paf -t 4
This command map all the fast5 and blow5 reads in /path/to/yeast/fast5_or_blow5/dir and its subdirectories to the yeast genome using 4 threads. The output will be saved to yeast_mapping.paf in a modified PAF format used by Uncalled.
Many other parameters can be found in the help information:
./sigmap -h
It is possible that your reads in fast5 files are compressed with the VBZ compression from Nanopore. Then you have to download the proper HDF5 plugin from here and make sure it can be found by your HDF5 library:
export HDF5_PLUGIN_PATH=/path/to/hdf5/plugins/lib
Getting help
If you encounter bugs or have further questions or requests, you can raise an issue at the issue page or contact me by email hwzhang@gatech.edu.
Citing Sigmap
If you use Sigmap, please cite:
Zhang, H., Li, H., Jain, C., Cheng, H., Au, K. F., Li, H., & Aluru, S. (2021). Real-time mapping of nanopore raw signals. Bioinformatics, 37(Supplement_1), i477-i483. https://doi.org/10.1093/bioinformatics/btab264