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