The SPAdes genome assembler has become the de facto standard de novo genome assembler for Illumina whole genome sequencing data of bacteria and other small microbes. SPAdes was a major improvement over previous assemblers like Velvet, but some of its components can be slow and it traditionally did not handle overlapping paired-end reads well.
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.
⚠️ Shovill is for isolate data only, primarily small haploid organisms. It will NOT work on metagenomes or larger genomes. Please use Megahit directly instead.
See which versions are available:
$ module avail shovill
Load one version into your environment and run it:
$ module load shovill/1.1.0 $ shovill
Notes from the sysadmin during installation:
$ cd /tmp $ git clone https://github.com/tseemann/shovill.git -b v1.1.0 $ sudo mkdir -p /export/apps/shovill/1.1.0 $ sudo cp -r shovill/* /export/apps/shovill/1.1.0
Test with:
$ module load shovill/1.1.0
Loading shovill/1.1.0
Loading requirement: spades/3.15 megahit/1.2.9 skesa/2.5.1 velvet/1.2.10 lighter/1.1.2 flash/1.2.11 htslib/1.11 samtools/1.11 bwa/0.7.18 kmc/3.1.1 seqtk/1.4 pilon/1.24
trimmomatic/0.39 samclip/0.4.0
$ shovill --version
shovill 1.1.0
$ shovill --check
[shovill] Using bwa - /export/apps/bwa/0.7.18/bin/bwa | Version: 0.7.18-r1243-dirty
[shovill] Using flash - /export/apps/flash/1.2.11/flash | FLASH v1.2.11
[shovill] Using java - /usr/bin/java | openjdk version "11.0.20.1" 2023-08-24 LTS
[shovill] Using kmc - /export/apps/kmc/3.1.1/bin/kmc | K-Mer Counter (KMC) ver. 3.1.1 (2019-05-19)
[shovill] Using lighter - /export/apps/lighter/1.1.2/bin/lighter | Lighter v1.1.2
[shovill] Using megahit - /export/apps/megahit/1.2.9/bin/megahit | MEGAHIT v1.2.9
[shovill] Using megahit_toolkit - /export/apps/megahit/1.2.9/bin/megahit_toolkit | v1.2.9
[shovill] Using pigz - /usr/bin/pigz | pigz 2.4
[shovill] Using pilon - /export/apps/pilon/1.24/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
[shovill] Using samclip - /export/apps/samclip/0.4.0/bin/samclip | samclip 0.4.0
[shovill] Using samtools - /export/apps/samtools/1.11/bin/samtools | Version: 1.11 (using htslib 1.11)
[shovill] Using seqtk - /export/apps/seqtk/1.4/bin/seqtk | Version: 1.4-r122
[shovill] Using skesa - /export/apps/skesa/2.5.1/bin/skesa | SKESA 2.5.1
[shovill] Using spades.py - /export/apps/spades/3.15/bin/spades.py | SPAdes genome assembler v3.15.5
[shovill] Using trimmomatic - /export/apps/trimmomatic/0.39/trimmomatic | 0.39
[shovill] Using velvetg - /export/apps/velvet/1.2.10/velvetg | Version 1.2.10
[shovill] Using velveth - /export/apps/velvet/1.2.10/velveth | Version 1.2.10