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Shovill v1.1.0 docker image

Main tool : Shovill

Additional tools:

  • SPAdes 3.15.5
  • SKESA 2.3.0
  • megahit 1.1.4
  • velvet 1.2.10
  • seqtk 1.3
  • kmc 3.1.1
  • lighter 1.1.1
  • trimmomatic 0.39
  • bwa 0.7.17
  • pilon 1.24
  • samclip
  • perl 5.22.1
  • python 2.7.12
  • pigz

Full documentation: https://github.com/tseemann/shovill

Assemble bacterial isolate genomes from Illumina paired-end reads

NOTE ON DEC 2022 UPGRADES

The Shovill 1.1.0 docker image was originally developed in May 2020 using this the version of the dockerfile, commit 615d1cfeb4

This older docker image will be maintained under this docker image tag: staphb/shovill:1.1.0

The Shovill docker image has since been upgraded via Pull Request #511 which upgraded the following tools in the shovill 1.1.0 dockerfile. Other smaller changes were also introduced (see the PR for details)

  • upgraded spades from 3.14.1 to 3.15.5
  • upgraded pilon from 1.22 to 1.24
  • upgraded samtools from 1.10 to 1.16.1
  • upgraded trimmomatic from 0.38 to 0.39

This newer docker image will be maintained under the docker image tags: staphb/shovill:1.1.0-2022Dec & staphb/shovill:latest in an effort to preserve the older docker image & allow for users to more easily transition to the new docker image in their pipelines.

Example Usage

# run shovill on the test FASTQ files bundled with shovill
shovill --outdir /data/out.spades --assembler spades --R1 /shovill-1.1.0/test/R1.fq.gz --R2 /shovill-1.1.0/test/R2.fq.gz