Description

Assemble bacterial isolate genomes from Illumina paired-end reads

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input paired-end FastQ files

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

contigs (file)

The final assembly produced by Shovill

contigs.fa

corrections (file)

List of post-assembly corrections made by Shovill

shovill.corrections

log (file)

Full log file for bug reporting

shovill.log

raw_contigs (file)

Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)

{skesa,spades,megahit,velvet}.fasta

gfa (file)

Assembly graph produced by MEGAHIT, SPAdes, or Velvet

contigs.{fastg,gfa,LastGraph}
author
Github user rpetit3
get in touch
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Tools

shovill
GPL v2

Microbial assembly pipeline for Illumina paired-end reads

github.com/tseemann/shovill github.com/tseemann/shovill/blob/master/README.md