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)