Assemble bacterial isolate genomes from Illumina paired-end reads
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
List of input paired-end FastQ files
versions
File containing software versions
versions.yml
contigs
The final assembly produced by Shovill
contigs.fa
corrections
List of post-assembly corrections made by Shovill
shovill.corrections
log
Full log file for bug reporting
shovill.log
raw_contigs
Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)
{skesa,spades,megahit,velvet}.fasta
gfa
Assembly graph produced by MEGAHIT, SPAdes, or Velvet
contigs.{fastg,gfa,LastGraph}
Microbial assembly pipeline for Illumina paired-end reads
