p3-submit-genome-assembly¶
Submit a PATRIC Genome Assembly Job¶
p3-submit-genome-assembly [options] output-path output-name
Submit a set of one or more read libraries to the PATRIC genome assembly service.
Usage synopsis¶
p3-submit-genome-assembly [-h] output-path output-name
Submit an assembly job with output written to output-path and named
output-name.
The following options describe the inputs to the assembly:
--workspace-path-prefix STR Prefix for workspace pathnames as given
to library parameters.
--workspace-upload-path STR If local pathnames are given as library parameters,
upload the files to this directory in the workspace.
--overwrite If a file to be uploaded already exists in
the workspace, overwrite it on upload. Otherwise
we will not continue the service submission.
--paired-end-lib P1 P2 A paired end read library. May be repeated.
--interleaved-lib LIB An interleaved paired end read library. May be repeated.
--single-end-lib LIB A single end read library. May be repeated.
--srr-id STR Sequence Read Archive Run ID. May be repeated.
The following options describe the processing requested:
--recipe Assembly recipe. Defaults to auto.
Valid values are auto, unicycler, canu,
spades, meta-spades, plasmid-spades, single-cell
--trim-reads Trim reads before assembly
--racon-iter Number of racon polishing iterations (for long reads)
--pilon-iter Number of pilon polishing iterations (for short reads)
--min-contig-len Filter out short contigs in the final assembly.
--min-contig-cov Filter out contigs with low read depth
in the final assembly.
--genome-size Estimated genome size (for canu)
The following options describe the read libraries:
--platform STR The sequencing platform for the next read
library or libraries. Valid values are
infer, illumina, pacbio, nanopore, iontorrent
--read-orientation-inward The reads in the next read library face inward (defaults to true)
--read-orientation-outward The reads in the next read library face outward (defaults to false)