A workflow for viral mapping-based discovery in metagenomic samples.
PikaVirus is a bioinformatics best-practise analysis pipeline for metagenomic analysis following a new approach, based on eliminatory k-mer analysis, followed by assembly and posterior contig-binning.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
-
Install
nextflow -
Install any of
Docker,SingularityorPodmanfor full pipeline reproducibility (please only useCondaas a last resort; see docs) -
Download the pipeline and test it on a minimal dataset with a single command:
nextflow run nf-core/pikavirus -profile test,<docker/singularity/podman/conda/institute>
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>in your command. This will enable eitherdockerorsingularityand set the appropriate execution settings for your local compute environment. -
Start running your own analysis!
nextflow run nf-core/pikavirus -profile <docker/singularity/podman/conda> --input '*_R{1,2}.fastq.gz'
See usage docs for all of the available options when running the pipeline.
By default, the pipeline currently performs the following:
- Sequencing quality control (
FastQC) - Trimming of low-quality regions in the reads (
FastP) - Trimmed sequences quality control (
FastQC) - Identification isolation of viral, bacterial, fungal and unknown reads (
Kraken2) - Assembly of unknow reads (
MetaQuast) and mapping against databases (Kaiju) to identify new possible pathogens - Selection of suitable viral, bacterial and fungal references from the provided directory (
MASH) - Alignment of viral, bacterial and fungal reads against reference genomes to ensure the presence of certain organisms (
Bowtie2)
The PikaVirus pipeline comes with documentation about the pipeline: usage and output.
Composed of a datasheet obtained from the NCBI. Versatile, though huge. Instructions on how to download it
PikaVirus requires a big database. A huge one in fact. However, thats why the Download_assembly.py script exists. This script will download all the viral, fungal or bacterial databases available in RefSeq, GenBank or both.
While testing, we have come across some assemblies that did not gather the necessary requirements for the optimal functioning of PikaVirus. Here is a list of all of them so far, and the reasons we have tagged them as excludable.
| Assembly | Reason for exclusion |
|---|---|
| GCA_006449155.1 | Assembly too short (20 pb) |
| GCA_006449195.1 | Assembly too short (27 pb) |
| GCA_006449235.1 | Assembly too short (32 bp) |
| GCA_006449275.1 | Assembly too short (44 bp) |
| GCA_006449355.1 | Assembly too short (25 bp) |
| GCA_006449395.1 | Assembly too short (18 bp) |
| GCA_006449175.1 | Assembly too short (17 bp) |
| GCA_006449215.1 | Assembly too short (20 bp) |
| GCA_006449255.1 | Assembly too short (32 bp) |
| GCA_006449335.1 | Assembly too short (12 bp) |
| GCA_006449375.1 | Assembly too short (17 bp) |
| GCA_006449415.1 | Assembly too short (19 bp) |
| GCA_001857805.1 | No identification potential |
| GCA_001857825.1 | No identification potential |
| GCA_001857745.1 | No identification potential |
| GCA_001857805.1 | No identification potential |
| GCA_001857825.1 | No identification potential |
| GCA_013086015.1 | No identification potential |
| GCA_013088685.1 | No identification potential |
| GCA_013088695.1 | No identification potential |
| GCA_013088705.1 | No identification potential |
| GCA_013088715.1 | No identification potential |
| GCA_013088725.1 | No identification potential |
| GCA_013088735.1 | No identification potential |
| GCA_013088745.1 | No identification potential |
| GCA_013088755.1 | No identification potential |
| GCA_013088765.1 | No identification potential |
| GCA_013088775.1 | No identification potential |
| GCA_013088785.1 | No identification potential |
| GCA_013088795.1 | No identification potential |
| GCA_013088805.1 | No identification potential |
| GCA_013088815.1 | No identification potential |
| GCA_013088825.1 | No identification potential |
| GCA_013088835.1 | No identification potential |
| GCA_013088845.1 | No identification potential |
| GCA_013088855.1 | No identification potential |
| GCA_013088865.1 | No identification potential |
| GCA_013088875.1 | No identification potential |
| GCA_013088885.1 | No identification potential |
| GCA_013088895.1 | No identification potential |
| GCA_013088905.1 | No identification potential |
| GCA_013088915.1 | No identification potential |
| GCA_013088925.1 | No identification potential |
| GCA_013088935.1 | No identification potential |
| GCA_013088945.1 | No identification potential |
| GCA_013088955.1 | No identification potential |
| GCA_013088965.1 | No identification potential |
| GCA_013088975.1 | No identification potential |
| GCA_013088985.1 | No identification potential |
| GCA_013088995.1 | No identification potential |
| GCA_013089005.1 | No identification potential |
| GCA_013089015.1 | No identification potential |
| GCA_013089025.1 | No identification potential |
| GCA_013089035.1 | No identification potential |
| GCA_013089045.1 | No identification potential |
| GCA_013089055.1 | No identification potential |
| GCA_013089065.1 | No identification potential |
| GCA_013089075.1 | No identification potential |
| GCA_013089085.1 | No identification potential |
| GCA_013089095.1 | No identification potential |
| GCA_013089105.1 | No identification potential |
| GCA_013089115.1 | No identification potential |
| GCA_013089125.1 | No identification potential |
| GCA_013089135.1 | No identification potential |
| GCA_013089145.1 | No identification potential |
| GCA_013089155.1 | No identification potential |
| GCA_013089165.1 | No identification potential |
| GCA_013089175.1 | No identification potential |
| GCA_013089185.1 | No identification potential |
| GCA_013089195.1 | No identification potential |
| GCA_013089205.1 | No identification potential |
| GCA_013089215.1 | No identification potential |
| GCA_013089225.1 | No identification potential |
| GCA_013089235.1 | No identification potential |
| GCA_013089245.1 | No identification potential |
| GCA_013089255.1 | No identification potential |
| GCA_013089265.1 | No identification potential |
| GCA_013089275.1 | No identification potential |
| GCA_013089285.1 | No identification potential |
| GCA_013089295.1 | No identification potential |
| GCA_013089305.1 | No identification potential |
| GCA_013089315.1 | No identification potential |
| GCA_013089325.1 | No identification potential |
| GCA_013089335.1 | No identification potential |
| GCA_013089345.1 | No identification potential |
| GCA_013089355.1 | No identification potential |
| GCA_013089365.1 | No identification potential |
| GCA_013089375.1 | No identification potential |
| GCA_013089385.1 | No identification potential |
| GCA_013089395.1 | No identification potential |
| GCA_013089405.1 | No identification potential |
| GCA_013089415.1 | No identification potential |
| GCA_013089425.1 | No identification potential |
| GCA_013089435.1 | No identification potential |
| GCA_013089445.1 | No identification potential |
| GCA_013089455.1 | No identification potential |
| GCA_013089465.1 | No identification potential |
| GCA_013089475.1 | No identification potential |
| GCA_013089485.1 | No identification potential |
| GCA_013089495.1 | No identification potential |
| GCA_013089505.1 | No identification potential |
| GCA_013089515.1 | No identification potential |
| GCA_013089525.1 | No identification potential |
| GCA_013089535.1 | No identification potential |
| GCA_013089545.1 | No identification potential |
| GCA_013089555.1 | No identification potential |
| GCA_013089565.1 | No identification potential |
| GCA_013089575.1 | No identification potential |
| GCA_013089585.1 | No identification potential |
| GCA_013089595.1 | No identification potential |
| GCA_013089605.1 | No identification potential |
| GCA_013089615.1 | No identification potential |
| GCA_013089625.1 | No identification potential |
| GCA_013089635.1 | No identification potential |
| GCA_013089645.1 | No identification potential |
| GCA_013089655.1 | No identification potential |
| GCA_013089665.1 | No identification potential |
| GCA_013089675.1 | No identification potential |
| GCA_013089685.1 | No identification potential |
| GCA_013089695.1 | No identification potential |
| GCA_013089705.1 | No identification potential |
| GCA_013089715.1 | No identification potential |
| GCA_013089725.1 | No identification potential |
| GCA_013089735.1 | No identification potential |
| GCA_013089745.1 | No identification potential |
| GCA_013089755.1 | No identification potential |
| GCA_013089765.1 | No identification potential |
| GCA_013089775.1 | No identification potential |
| GCA_013089785.1 | No identification potential |
| GCA_013089795.1 | No identification potential |
| GCA_013089805.1 | No identification potential |
| GCA_013089815.1 | No identification potential |
| GCA_013089825.1 | No identification potential |
| GCA_013089835.1 | No identification potential |
| GCA_013089845.1 | No identification potential |
| GCA_013089855.1 | No identification potential |
| GCA_013089865.1 | No identification potential |
| GCA_013089875.1 | No identification potential |
| GCA_013089885.1 | No identification potential |
| GCA_013089895.1 | No identification potential |
| GCA_013089905.1 | No identification potential |
| GCA_013089915.1 | No identification potential |
| GCA_013089925.1 | No identification potential |
| GCA_013089935.1 | No identification potential |
| GCA_013089945.1 | No identification potential |
| GCA_013089955.1 | No identification potential |
| GCA_013089965.1 | No identification potential |
| GCA_013089975.1 | No identification potential |
| GCA_013089985.1 | No identification potential |
| GCA_013089995.1 | No identification potential |
| GCA_013090005.1 | No identification potential |
| GCA_013090015.1 | No identification potential |
| GCA_013090025.1 | No identification potential |
| GCA_013090035.1 | No identification potential |
| GCA_013090045.1 | No identification potential |
| GCA_013096315.1 | No identification potential |
NOTE: some of these assemblies may have been removed from the NCBI. In addition, there might be a lot of other assemblies.
PikaVirus 2.0 was originally written by Guillermo Jorge Gorines Cordero, under supervision of the BU-ISCIII team in Madrid, Spain.
PikaVirus has been developed under the nf-core community guidelines, tools and best practises, despite not being an official nf-core pipeline. You can cite the nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. ReadCube: Full Access Link
We thank the following people for their extensive assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
In addition, references of tools and data used in this pipeline are as follows:
Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu & Ben Langmead.
Genome biology 2019 Nov 28. doi: 10.1186/s13059-019-1891-0
fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu.
Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890,. doi: 10.1093/bioinformatics/bty560
Bioconda: sustainable and comprehensive software distribution for the life sciences
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster & The Bioconda Team
Nature Methods volume 15, pages 475–476(2018). doi 10.1038/s41592-018-0046-7
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren & Adam M. Phillippy
Genome Biology 17, Article number: 132 (2016). doi 10.1186/s13059-016-0997-x