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Installation

Install Nextflow

The VSD workflow requires Nextflow to be installed in your account on the HPC. Find details on how to install and test Nextflow here prepare a nextflow.config file and run a PBS pro submission script for Nextflow pipelines.

Pull the git repo using:

nextflow pull command then add -r vsd-1.0

Install conda3 or miniconda3

https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

All the required modules are included in the environment.yml file in the pipeline base directory and shows all the tools used in the pipeline:

name: vsd-1.0
channels:
  - bioconda
  - conda-forge
  - defaults
  - r
  - anaconda
dependencies:
  - blast=2.11.0
  - cap3=10.2011
  - spades=3.14.0
  - emboss=6.6.0
  - openjdk=8.0.152
  - fastp=0.20.1
  - biopython=1.76
  - numpy=1.16.5
  - matplotlib=2.2.3
  - velvet=1.2.10
  - bowtie=1.3.0
  - samtools=1.12
  - picard==2.25.6
  - bedtools
  - bcftools
  - pandas
  - fastqc=0.11.9
  - fastp=0.20.1
  - cutadapt=3.5
  - umi_tools=1.1.2

Install a local NCBI blast directory (NT and NR)

Find detailed infor on how to download these databases at https://www.ncbi.nlm.nih.gov/books/NBK569850/

Make sure the taxdb.btd and the taxdb.bti files are also present in the directory.

Create a folder where you will store your NCBI database including the date of download. For instance:

mkdir blastDB/30112021

Run the following PBS script in the newly created folder. Use the update_blastdb.pl script from the blast+ version you will use with your pipeline.

#!/bin/bash -l
#PBS -N blastdb_download
#PBS -l walltime=24:00:00
#PBS -l mem=60gb
#PBS -l ncpus=2

cd $PBS_O_WORKDIR
perl update_blastdb.pl --decompress nt [*]
perl update_blastdb.pl --decompress nr [*]
perl update_blastdb.pl taxdb
tar -xzf taxdb.tar.gz

The VSD workflow

The VSD workflow will perform the following steps by default:

  • Retain reads of a given length (e.g. 21-22 or 24 nt long) from fastq file(s) provided in index.csv file (readprocessing)

  • De novo assembly using kmer 15 and coverage 3 (velvet)

  • Collapse contigs into scaffolds (min length 20) (cap3)

  • Run megablast homology search against NCBI NT database (megablast_nt_velvet)

  • Summarise megablast results and restrict to virus and viroid matches (BlastTools_megablast_velvet)

  • Derive coverage statistics, consensus sequence and VCF matching to top blast hits (filter_n_cov)

A number of additional optional steps can be run:

  • --blastp: Predict ORF from de novo assembly (derived with Velvet) and run blastP againts NCBI NR (getorf, blastp, blastpdbcmd, BlastToolsp) --blastp

  • --contamination_detection: Run cross-sample contamination prediction (contamination_detection)

  • --blastlocaldb: Run blastn and megablast homology search on de novo assembly (derived with Velvet) against local virus and viroid database (blast_nt_localdb_velvet, filter_blast_nt_localdb_velvet)

  • --blastn: Run blastn homology search on de novo assembly (derived with Velvet) against local virus and viroid database (blastn_nt_velvet)

  • --spades: Run SPAdes 3.14 de novo assembler and perform blastn homology analysis on the derived de novo contigs (spades, cap3_spades, megablast_nt_spades , BlastToolsn_megablast_spades)

A number of additional options are included:

  • --targets: A text file with the taxonomy of the viruses/virioids of interest can be provided and only these will be retained in the megablast summary results derived at the filter_n_cov step.

  • --spadeskmer specifies the range of kmers to use when running spades

  • --cap3_len specifies the minimal length of contigs to retain after CAP3 scaffolding

  • --blastn_evalue and --blastp_evalue specifies the evalue parameter to use during blast analyses

  • --orf_minsize correspond to the minimal open reading frame getorf retains

To enable these options, they can either be included in the nextflow run command provided in the PBS script: 

nextflow run $PBS_O_WORKDIR/main.nf -resume  --indexfile $PBS_O_WORKDIR/index_example.csv --blastlocaldb --spades --contamination_detection

or update parameter to true in the nextflow.config file. For instance:

params {
blastlocaldb = true
spades = true
contamination_detection = true
}

Preparing the data

Preparing a index.csv file

You need to create a TAB delimited text file that will be the input for the workflow. By default the pipeline will look for a file called “index.csv” in the base directory but you can specify any file name using the --indexfile [filename] in the nextflow run command. This text file requires the following columns (which needs to be included as a header): sampleid,samplepath,minlen,maxlen:

  • sampleid will be the sample name that will be given to the files created by the pipeline

  • samplepath is the full path to the quality filtered fastq files that the pipeline requires as starting input

  • minlen and maxlen correspond to the read size that will be retained for downstream analyses.

An index_example.csv is included in the base directory:

sampleid,samplepath,minlen,maxlen
MT212,/work/hia_mt18005/diagnostics/2021/14_RAMACIOTTI_LEL9742-LEL9751/results/06_usable_reads/MT212_21-22bp.fastq,21,22
MT213,/work/hia_mt18005/diagnostics/2021/14_RAMACIOTTI_LEL9742-LEL9751/results/06_usable_reads/MT213_21-22bp.fastq,21,22

You also need to provide the path of your NCBI blast directory in the nextflow.config file. For instance:

params {
  blast_db = '/lustre/work-lustre/hia_mt18005/blastDB/30112021'
  }

If you are interested to run a blast analysis against a local database, you also need to specify its path in the nextflow.config file. For example:

blastn_local_db = '/work/hia_mt18005/databases/PVirDB/PVriDB_ver2021_11_09/PVirDB_ver20211109.fasta'

Running the pipeline

Finally you need to create a PBS script which includes your nextflow run command. An example of PBS script is included in the base directory and will run the pipeline with default steps:

#!/bin/bash -l
#PBS -N NextflowVSD
#PBS -l select=1:ncpus=2:mem=6gb
#PBS -l walltime=24:00:00


cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run $PBS_O_WORKDIR/main.nf -resume  --indexfile $PBS_O_WORKDIR/index_example.csv

This following PBS script will additionally run spades, the cross sample predictor and blast searches against a local database:

#!/bin/bash -l
#PBS -N NextflowVSD
#PBS -l select=1:ncpus=2:mem=6gb
#PBS -l walltime=24:00:00

#run spades
#run blast homology against user local database 
#run false positive predictor
nextflow run $PBS_O_WORKDIR/main.nf -resume  --indexfile $PBS_O_WORKDIR/index_example.csv --blastlocaldb --spades --contamination_detection

These jobs can be submitted using:

qsub nextflow_example.pbs

Monitoring the run

You can use the command

qstat -u $USER

Alternatively use the following command:

qjobs

To check on the jobs you are running. Nextflow will launch additional jobs during the run.

You can also check the .nextflow.log file for details on what is going on.

Finally, if you have configured the connection to the NFTower you can logon and check your run.

Outputs

Under the results folder, the pipeline will populate outputs under separate folders for each step. These will be stored in subfolders for each sample:

results → 01_read_size_selection → sample1

→ sample2

→ sample 3

→ 02_velvet → sample1

→ sample2

→ sample 3

etc…

The folders are:

  • 01_read_size_selection (cutadapt log file and fastq file including reads only matching the size specified in the index.csv file) MT020_21-22nt_cutadapt.log & MT020_21-22nt.fastq

  • 02_velvet (velvet results and the fasta file which includes the velvet assembled contigs MT020_velvet_assembly_21-22nt.fasta

  • 02a_spades (if spades is additionally run)

  • 03_cap3 (fasta file of the scaffolds produced by CAP3 as well as the singletons) MT020_velvet_cap3_21-22nt_rename.fasta

  • 04_blastn (all blastn results, filtered results limited to only viruses and viroid top 5 hit matches and their taxonomy) MT020_velvet_21-22nt_megablast_vs_NT.bls, MT020_velvet_21-22nt_megablast_vs_NT_top5Hits.txt, MT020_velvet_21-22nt_megablast_vs_NT_top5Hits_virus_viroids_final.txt MT020_velvet_21-22nt_megablast_vs_NT_top5Hits_virus_viroids_seq_ids_taxonomy.txt

  • 05_blastoutputs (BlastTools.jar summary output which clusters all the contigs matching to a specific hit. summary_MT029_velvet_21-22nt_megablast_vs_NT_top5Hits_virus_viroids_final.txt

  • 06_blastp (blastp outputs)

  • 07_filternstats (filtered blast summary with various coverage statistics for each virus and viroid hit, and associated consensus fasta file and vcf file) MT020_21-22nt_top_scoring_targets_with_cov_stats.txt, MT020_21-22nt_MK929590_Peach_latent_mosaic_viroid.consensus.fasta, MT020_21-22nt_MK929590_Peach_latent_mosaic_viroid_sequence_variants.vcf.gz

  • 08_report (summary of results for all samples included in the index.csv file. This includes a cross-contamination prediction) run_top_scoring_targets_with_cov_stats_with_cont_flag_21-22nt_0.01.txt

To do:

  • Include a deduplication step for fastq files that have UMIs incorporated

  • Make QC filtering optional

  • Work on final report

  • Add coverage statistics to local db blast results

  • Incorporate VirusDetect in the pipeline

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