Task: assemble

Task: assemble

This task assembles reads using the SPAdes assembler. It assembles the input reads using the options --careful --only-assembler and (by default) uses the kmers 127,121,111,101,95,91,85,81,75,71. It uses the assembly from the first kmer where SPAdes finishes successfully.

Usage and options

The general usage is

circlator assemble [options] <in.reads.fasta> <out_directory>

There are the folowing options:

• --threads INT: number of threads (the -t option to spades). Default: 1.
• --verbose: be verbose.
• --spades_k k1,k2,k3,...: comma separated list of kmers to use when running SPAdes. Max kmer is 127 and each kmer should be an odd integer. Default: 127,121,111,101,95,91,85,81,75,71.

Output files

The output directory out_directory/ is the direct output of SPAdes, from the kmer used that made a successful assembly (failed assemblies are deleted).