![]() The Canu Parameter Reference, but the common ones are described in this document. SI prefixes allowed, for example, 4.7m or 2.8g see genomeSize). One parameter is required: the genomeSize (in bases, with common Memory, threads, grid), algorithmic parameters (e.g., error rates, trimming aggressiveness), andĮnable or disable entire processing steps (e.g., don’t correct errors, don’t search for subreads). Parameters are key=value pairs that configure the assembler. Specifying reads as -corrected -untrimmed will run only the assembly step. Will run only the trimming and assembling stages. We do exactly that in the Canu Quick Start.Īdditionally, suppling pre-corrected reads with -pacbio -corrected or -nanopore -corrected Reads once and try many different assemblies. These options can be useful if you want to correct Specifying your read characteristics and a step name. ![]() It is possible to run exactly one task by Setting commonly used parameters, but overriding them for specific assemblies.īy 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). Parameters will be applied before any from the command line are used, providing a method for The -s option will import a list of parameters from the supplied specification (‘spec’) file. It is _not_ possible to run two different Not supplied, canu will run in the current directory, otherwise, Canu will create theĪssembly-directory and run in that directory. ![]() The -p option, to set the file name prefix of intermediate and output files, is mandatory.
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