Polypolish
Polypolish is a tool for polishing genome assemblies with short reads. Unlike
other tools in this category, Polypolish uses SAM files where each read has
been aligned to all possible locations (not just a single best location).
This allows it to repair errors in repeat regions that other alignment-based
polishers cannot fix.
For installation instructions, usage, deeper explanations and more, head over
to the Polypolish wiki!
Location and version:
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$ which polypolish
/local/cluster/polypolish/polypolish
$ polypolish --version
Polypolish v0.5.0
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help message:
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$ polypolish --help
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Polypolish v0.5.0
short-read polishing of long-read assemblies
github.com/rrwick/Polypolish
USAGE:
polypolish [OPTIONS] <ASSEMBLY> <SAM>...
ARGS:
<ASSEMBLY> Assembly to polish (one file in FASTA format)
<SAM>... Short read alignments (one or more files in SAM
format)
OPTIONS:
-d, --min_depth <MIN_DEPTH>
A base must occur at least this many times in the pileup to
be considered valid [default: 5]
--debug <DEBUG>
Optional file to store per-base information for debugging
purposes
-h, --help
Print help information
-i, --fraction_invalid <FRACTION_INVALID>
A base must make up less than this fraction of the read depth
to be considered invalid [default: 0.2]
-m, --max_errors <MAX_ERRORS>
Ignore alignments with more than this many mismatches and
indels [default: 10]
-v, --fraction_valid <FRACTION_VALID>
A base must make up at least this fraction of the read depth
to be considered valid [default: 0.5]
-V, --version
Print version information
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software ref: https://github.com/rrwick/Polypolish
software ref: https://github.com/rrwick/Polypolish/wiki
research ref: https://doi.org/10.1371/journal.pcbi.1009802