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@@ -32,12 +32,13 @@ such as reformatting files, but generally just executes other programs.
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::
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canu [-trimmed|-untrimmed|-raw|-corrected] \
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[-s <assembly-specifications-file>] \
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canu [-haplotype|-correct|-trim] \
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[-s <assembly-specifications-file>] \
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-p <assembly-prefix> \
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-d <assembly-directory> \
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genomeSize=<number>[g|m|k] \
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[other-options] \
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[-trimmed|-untrimmed|-raw|-corrected] \
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[-pacbio|-nanopore|-pacbio-hifi] *fastq
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The -p option, to set the file name prefix of intermediate and output files, is mandatory. If -d is
@@ -50,7 +51,7 @@ parameters will be applied before any from the command line are used, providing
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setting commonly used parameters, but overriding them for specific assemblies.
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By default, all needed top-level tasks are performed (-pacbio and -nanopore are assumed to be raw and untrimmed while -pacbio-hifi are assumed to be corrected and trimmed). It is possible to run exactly one task by
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specifying your read characteristics. These options can be useful if you want to correct
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specifying your read characteristics and a step name. These options can be useful if you want to correct
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reads once and try many different assemblies. We do exactly that in the :ref:`quickstart`.
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Additionally, suppling pre-corrected reads with -pacbio -corrected or -nanopore -corrected
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will run only the trimming and assembling stages. Specifying reads as -corrected -untrimmed will run only the assembly step.
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