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assembler/src/projects/pathracer/README.md

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_In addition:_ Some other developer options that are not supposed to be tuned by end-user. Could be removed in further releases.
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### Output
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For each input pHMM (genemode ) PathRacer reports:
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For each input pHMM (gene model) PathRacer reports:
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- **<gene\_name>.seqs.fa**: sequences correspondent to _N_ best scored paths ordered by score along with their alignment in CIGAR format
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- **<gene\_name>.nucls.fa**: _(for amino acids pHHMs only)_ the same sequences in nucleotides
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### Examples
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One can download example datasets from here <http://cab.spbu.ru/software/pathracer/>
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One can download example datasets from <http://cab.spbu.ru/software/pathracer/>
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- **urban_strain.gfa**: strain assembly graph of Singapore clinical isolation ward wastewater metagenome (SRA accession SRR5997548, dataset H1)
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- **bla\_all.hmm**: 159 beta-lactamase family pHMMs from **AMRFinder** database <https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/>

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