PathRacer is a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies.
PathRacer is implemented on top of SPAdes and will be available soon as a part of SPAdes package. For now one can download, build, and try pre-release version of SPAdes package including PathRacer
Experiment version of PathRacer supporting minigraph gfa-files is available here
See the main SPAdes page for system requirements and build instruction. Manual could be found here.
- beta-lactamases: HMM file (159 hmms), Xander/MegaGTA database, sequences
- ribosomal RNA: HMM file, 16s sequences from SYNTH metagenome dataset
- ONT-assembled plasmids from Li et al, 2018