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, 117, 107, 97, 87, 77. It uses the assembly that has the largest N50.

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: 127,117,107,97,87,77.
• --spades_use_first: Use the first successful SPAdes assembly. Default is to try all kmers and use the assembly with the largest N50.
• --not_careful: Do not use the --careful option with SPAdes (used by default)
• --not_only_assembler: Do not use the --assemble-only option with SPAdes (used by default)

Output files

The output directory out_directory/ is the direct output of SPAdes, from the kmer that had the largest N50 (failed assemblies are deleted).