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Task: all
This task runs the complete Circlator pipeline. To get going quickly, read the brief instructions.
The general usage is
circlator all [options] <assembly.fasta> <reads.fasta> <output directory>
This runs the tasks: progcheck, mapreads, bam2reads, assemble, merge, clean, fixstart. Options to the individual tasks can be changed. Run
circlator all --help
to see all the options. Please see each individual task page for a description of each the options.
Each task has its own options, for example, the kmers used when assembling with SPAdes can be changed when running the assemble task using the option --spades_k 99. But, most task options can also be changed when running the whole Circlator pipeline with one call. The corresponding option when running the entire pipeline is --assemble_spades_k, ie it has the same name, but with assemble_ prepended. All other options (where applicable) are named in a similar manner.
First, a copy of the input assembly is taken, with names edited so that everything after the first whitespace is removed. If this leads to non-unique names then Circlator will stop with an error, and list the offending contig names. If successful, the new file is called 00.input_assembly.fasta and is indexed with samtools faidx to make the file 00.input_assembly.fasta.fai.
These files are the output of running circlator mapreads.
See the mapreads page for more information.
These files are the output of running circlator bam2reads.
See the bam2reads page for more information.
The directory 03.assembly is the output of running circlator assemble.
See the assemble page for more information.
These files are the output of running circlator merge.
See the merge page for more information.
These files are the output of running circlator clean.
See the clean page for more information.
The exception is 05.clean.contigs_to_keep, which is a file of the names of contigs
that were identified as circular when running the task merge. This is used
as input to the clean stage using the option --keep 05.clean.contigs_to_keep, so
that these contigs will not be removed from the assembly.
These files are the output of running circlator fixstart.
See the fixstart page for more information.
The exception is the file 06.fixstart.contigs_to_not_change of names of contigs
that were not identified as circular when the merge stage was run. This is used as
input to the fixstart stage using the option --ignore 06.fixstart.contigs_to_not_change,
so that these contigs do not have their start positions changed.