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| {"name":"polypolish","description":"short-read polishing of long-read assemblies","usage":"polypolish [OPTIONS] <ASSEMBLY> <SAM>...","options":[{"names":["-d","--min_depth"],"argument":"<MIN_DEPTH>","description":"A base must occur at least this many times in the pileup to be considered valid [default: 5]"},{"names":["--debug"],"argument":"<DEBUG>","description":"Optional file to store per-base information for debugging purposes"},{"names":["-h","--help"],"argument":"","description":"Print help information"},{"names":["-i","--fraction_invalid"],"argument":"<FRACTION_INVALID>","description":"A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"},{"names":["-m","--max_errors"],"argument":"<MAX_ERRORS>","description":"Ignore alignments with more than this many mismatches and indels [default: 10]"},{"names":["-v","--fraction_valid"],"argument":"<FRACTION_VALID>","description":"A base must make up at least this fraction of the read depth to be considered valid [default: 0.5]"},{"names":["-V","--version"],"argument":"","description":"Print version information"}],"version":"Polypolish v0.5.0"} | ||
| {"name":"polypolish","description":"short-read polishing of long-read assemblies","usage":"polypolish <COMMAND>","options":[{"names":["-h","--help"],"argument":"","description":"Print help"},{"names":["-V","--version"],"argument":"","description":"Print version"}],"subcommands":[{"name":"filter","description":"filter paired-end alignments based on insert size","usage":"polypolish filter [OPTIONS] --in1 <IN1> --in2 <IN2> --out1 <OUT1> --out2 <OUT2>","options":[{"names":["--in1"],"argument":"<IN1>","description":"Input SAM file - first read in pairs"},{"names":["--in2"],"argument":"<IN2>","description":"Input SAM file - first second in pairs"},{"names":["--out1"],"argument":"<OUT1>","description":"Output SAM file - first read in pairs"},{"names":["--out2"],"argument":"<OUT2>","description":"Output SAM file - first second in pairs"},{"names":["--orientation"],"argument":"<ORIENTATION>","description":"Expected pair orientation [default: auto]"},{"names":["--low"],"argument":"<LOW>","description":"Low percentile threshold [default: 0.1]"},{"names":["--high"],"argument":"<HIGH>","description":"High percentile threshold [default: 99.9]"},{"names":["-h","--help"],"argument":"","description":"Print help"},{"names":["-V","--version"],"argument":"","description":"Print version"}]},{"name":"polish","description":"polish a long-read assembly using short-read alignments","usage":"polypolish polish [OPTIONS] <ASSEMBLY> [SAM]...","options":[{"names":["--debug"],"argument":"<DEBUG>","description":"Optional file to store per-base information for debugging purposes"},{"names":["-i","--fraction_invalid"],"argument":"<FRACTION_INVALID>","description":"A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"},{"names":["-v","--fraction_valid"],"argument":"<FRACTION_VALID>","description":"A base must make up at least this fraction of the read depth to be considered valid [default: 0.5]"},{"names":["-m","--max_errors"],"argument":"<MAX_ERRORS>","description":"Ignore alignments with more than this many mismatches and indels [default: 10]"},{"names":["-d","--min_depth"],"argument":"<MIN_DEPTH>","description":"A base must occur at least this many times in the pileup to be considered valid [default: 5]"},{"names":["--careful"],"argument":"","description":"Ignore any reads with multiple alignments"},{"names":["-h","--help"],"argument":"","description":"Print help"},{"names":["-V","--version"],"argument":"","description":"Print version"}]}],"version":"Polypolish 0.6.0"} |
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| name: polypolish | ||
| description: short-read polishing of long-read assemblies | ||
| usage: polypolish [OPTIONS] <ASSEMBLY> <SAM>... | ||
| usage: polypolish <COMMAND> | ||
| options: | ||
| - names: | ||
| - -d | ||
| - --min_depth | ||
| argument: <MIN_DEPTH> | ||
| description: 'A base must occur at least this many times in the pileup to be considered valid [default: 5]' | ||
| - names: | ||
| - --debug | ||
| argument: <DEBUG> | ||
| description: Optional file to store per-base information for debugging purposes | ||
| - names: | ||
| - -h | ||
| - --help | ||
| argument: "" | ||
| description: Print help information | ||
| - names: | ||
| - -i | ||
| - --fraction_invalid | ||
| argument: <FRACTION_INVALID> | ||
| description: 'A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]' | ||
| - names: | ||
| - -m | ||
| - --max_errors | ||
| argument: <MAX_ERRORS> | ||
| description: 'Ignore alignments with more than this many mismatches and indels [default: 10]' | ||
| - names: | ||
| - -v | ||
| - --fraction_valid | ||
| argument: <FRACTION_VALID> | ||
| description: 'A base must make up at least this fraction of the read depth to be considered valid [default: 0.5]' | ||
| description: Print help | ||
| - names: | ||
| - -V | ||
| - --version | ||
| argument: "" | ||
| description: Print version information | ||
| version: Polypolish v0.5.0 | ||
| description: Print version | ||
| subcommands: | ||
| - name: filter | ||
| description: filter paired-end alignments based on insert size | ||
| usage: polypolish filter [OPTIONS] --in1 <IN1> --in2 <IN2> --out1 <OUT1> --out2 <OUT2> | ||
| options: | ||
| - names: | ||
| - --in1 | ||
| argument: <IN1> | ||
| description: Input SAM file - first read in pairs | ||
| - names: | ||
| - --in2 | ||
| argument: <IN2> | ||
| description: Input SAM file - first second in pairs | ||
| - names: | ||
| - --out1 | ||
| argument: <OUT1> | ||
| description: Output SAM file - first read in pairs | ||
| - names: | ||
| - --out2 | ||
| argument: <OUT2> | ||
| description: Output SAM file - first second in pairs | ||
| - names: | ||
| - --orientation | ||
| argument: <ORIENTATION> | ||
| description: 'Expected pair orientation [default: auto]' | ||
| - names: | ||
| - --low | ||
| argument: <LOW> | ||
| description: 'Low percentile threshold [default: 0.1]' | ||
| - names: | ||
| - --high | ||
| argument: <HIGH> | ||
| description: 'High percentile threshold [default: 99.9]' | ||
| - names: | ||
| - -h | ||
| - --help | ||
| argument: "" | ||
| description: Print help | ||
| - names: | ||
| - -V | ||
| - --version | ||
| argument: "" | ||
| description: Print version | ||
| - name: polish | ||
| description: polish a long-read assembly using short-read alignments | ||
| usage: polypolish polish [OPTIONS] <ASSEMBLY> [SAM]... | ||
| options: | ||
| - names: | ||
| - --debug | ||
| argument: <DEBUG> | ||
| description: Optional file to store per-base information for debugging purposes | ||
| - names: | ||
| - -i | ||
| - --fraction_invalid | ||
| argument: <FRACTION_INVALID> | ||
| description: 'A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]' | ||
| - names: | ||
| - -v | ||
| - --fraction_valid | ||
| argument: <FRACTION_VALID> | ||
| description: 'A base must make up at least this fraction of the read depth to be considered valid [default: 0.5]' | ||
| - names: | ||
| - -m | ||
| - --max_errors | ||
| argument: <MAX_ERRORS> | ||
| description: 'Ignore alignments with more than this many mismatches and indels [default: 10]' | ||
| - names: | ||
| - -d | ||
| - --min_depth | ||
| argument: <MIN_DEPTH> | ||
| description: 'A base must occur at least this many times in the pileup to be considered valid [default: 5]' | ||
| - names: | ||
| - --careful | ||
| argument: "" | ||
| description: Ignore any reads with multiple alignments | ||
| - names: | ||
| - -h | ||
| - --help | ||
| argument: "" | ||
| description: Print help | ||
| - names: | ||
| - -V | ||
| - --version | ||
| argument: "" | ||
| description: Print version | ||
| version: Polypolish 0.6.0 |
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