Ultra-careful amplicon-aware viral assembly for tiled amplicon schemes.
Please see the Viridian Wiki for full documentation.
Preprint: https://doi.org/10.1101/2024.04.29.591666
The recommended method is to use a pre-built Docker or Singularity container (see the wiki for how to build your own).
Both the Docker and Singularity container have the main script
viridian
installed.
Get a Docker image of the latest release:
docker pull ghcr.io/iqbal-lab-org/viridian:latest
All Docker images from v1.2.1 onwards are listed in the packages page. Older images can be found on the old packages page (viridian used to be called "viridian_workflow", and hence were put on a packages page called "viridian_workflow" by github).
Releases
include a Singularity image to download.
Each release from v1.2.1 onwards has a singularity image file called
viridian_vX.Y.Z.img
, where X.Y.Z
is the release version. Newer releases
also have an image for ARM architecture called viridian_vX.Y.Z.arm.img
.
Older images (from when viridian was called "viridian_workflow") are
called viridian_workflow_vX.Y.Z.img
.
These instructions assume that you are assembling SARS-CoV-2 data.
To run on paired Illumina reads:
viridian run_one_sample \
--tech illumina \
--reads1 reads_1.fastq.gz \
--reads2 reads_2.fastq.gz \
--outdir OUT
To run on unpaired nanopore reads:
viridian run_one_sample \
--tech ont \
--reads reads.fastq.gz \
--outdir OUT
To run on paired or unpaired Ion Torrent reads, use either of the
above commands, but with the option --tech iontorrent
.
Download reads with accession SRR12345678 and run:
viridian run_one_sample --run_accession SRR12345678 --outdir OUT
The sequencing tech and unpaired/paired is taken from the ENA metadata for each run.
Download and run on a batch of sequencing runs, using a file
runs.txt
of INSDC run accessions:
viridian dl_and_run --acc_file runs.txt --outdir OUT
The default files in the output directory are:
consensus.fa.gz
: a gzipped FASTA file of the consensus sequence.variants.vcf
: a VCF file of the identified variants between the consensus
sequence and the reference genome.log.json.gz
: a gzipped JSON file that contains logging information
for the viridian run.qc.tsv.gz
: a gzipped tab-delimited file of per-base QC informationscheme_id.depth_across_genome.pdf
: a plot of the read depth across
the genome, with amplicons coloured in the background.scheme_id.score_plot.pdf
: a plot of the scoring for amplicon scheme
identification.If the option --keep_bam
is used, then a sorted BAM file of the reads mapped
to the reference will also be present, called
reference_mapped.bam
(and its index file reference_mapped.bam.bai
).
--sample_name MY_NAME
: use this to change the sample name
(default is "sample") that is put in the final FASTA file, BAM file, and
VCF file.--reads_bam MY_READS.bam
: instead of providing FASTQ (or FASTA) files of
reads, you can provide a sorted by genome coordinate and indexed BAM file.
The reference genome must be the same as that used by viridian
(by default MN908947).--keep_bam
: use this option to keep the BAM file of original input reads
mapped to the reference genome.--decontam COVID
: decontaminate the reads using ReadItAndKeep at the
start of the pipeline (this is incompatible with --reads_bam
)--force
: use with caution - it will overwrite the output directory if
it already exists.--write_msa indel_as_ref
: this will write a FASTA file
called msa.indel_as_ref.fa
that can be
used to build trees. It has the consensus sequence aligned to the
reference genome, but with insertions in the consensus ignored and
deletions replaced with the reference sequence.--run_accession RUN_ID
: using this option will download the specified reads
from the ENA, and infer the --tech
option from the ENA metadata