Task: all

Task: all

This task runs the complete Circlator pipeline. To get going quickly, read the brief instructions.

Usage and options

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.

Output files

00.* - check input assembly

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.

01.mapreads.* - map reads to assembly

These files are the output of running circlator mapreads. See the mapreads page for more information.

02.bam2reads - extract reads for reassembly

These files are the output of running circlator bam2reads. See the bam2reads page for more information.

03.assembly - assembly of extracted reads

The directory 03.assembly is the output of running circlator assemble. See the assemble page for more information.

04.merge.* - merge and circularize

These files are the output of running circlator merge. See the merge page for more information.

05.clean.* - clean contigs

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.

06.fixstart.* - fix contig start positions

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.