With slorado, now you can do some nanopore basecalling on AMD GPUs. We have some compiled binaries which should work on Linux if you have GLIBC >= 2.28 (invoke ldd --version to check). You should also have the GPU driver installed. Currently, we have tested the binaries only on systems in Note 1. If you encounter a problem feel free to open an issue.
First, download and extract the slorado rocm Linux binaries tarball. Note that this is for testing only and the link will not be persistent!!!!
VERSION=v0.2.0-beta
wget "https://github.com/BonsonW/slorado/releases/download/$VERSION/slorado-$VERSION-x86_64-rocm-linux-binaries.tar.gz"
tar xvf slorado-$VERSION-x86_64-rocm-linux-binaries.tar.gz
cd slorado-$VERSION
bin/slorado --help
Download the test dataset with 20,000 reads and run slorado:
wget -O PGXXXX230339_reads_20k.blow5 https://slow5.bioinf.science/hg2_prom_5khz_subsubsample
./bin/slorado basecaller models/dna_r10.4.1_e8.2_400bps_hac@v4.2.0 PGXXXX230339_reads_20k.blow5 -o out.fastq -x cuda:all
Refer to troubleshoot for help on resolving common problems.
Test if the output maps and identity scores are good (required minimap2, the human genome and datamash):
minimap2 -cx map-ont hg38noAlt.fa out.fastq --secondary=no -t16 | awk '{print $10/$11}' | datamash mean 1 median 1 count 1
It should print the mean identity score, median identity score and the number of alignments. The numbers are expected to be close to the following (would not be identical due to floating point deviations):
0.94113261325097 0.9771185 24768
Currently, we have tested these binaries on following systems: