Integrated virus assembler (IVA) is a de novo assembler designed for virus genomes without repeat sequences, using Illumina read pairs from mixed populations at extremely high and variable depth.

References:

• Martin Hunt et al.. IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics 2015(31): 2374-2376. Pubmed |  PMC |  Journal

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• Module Name: iva (see the modules page for more information)
• iva is a multithreaded application. Please match the number of allocated CPUs to the number of threads
• some iva versions mis-report their version
• some samtools errors may be spurious

Allocate an interactive session and run the built in test data set

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=6g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load iva
[user@cn3144]$ iva --test --threads=2 --trimmomatic=$TRIMMOJAR test
Running iva in test mode...
Copied input test files into here: PREFIX/test
Current working directory: PREFIX/test
Running iva on the test data with the command:
/usr/local/lib/python3.6/dist-packages/iva-1.0.9-py3.6.egg/EGG-INFO/scripts/iva --threads 2 \
    --trimmomatic /Trimmomatic-0.38/trimmomatic-0.38.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
Finished running iva
Looks OK. Final output contigs file is: PREFIX/test/iva.out/contigs.fasta
[user@cn3144]$ tree test
test
|-- [user    672]  hiv_pcr_primers.fa
|-- [user   9.7K]  iva_contigs_no_trimmomatic.fasta
|-- [user   9.0K]  iva_contigs_with_trimmomatic.fasta
|-- [user   4.0K]  iva.out
|   |-- [user   3.1K]  adapters.fasta
|   |-- [user   9.8K]  contigs.fasta
|   `-- [user    369]  info.txt
|-- [user   3.6M]  reads_1.fq.gz
|-- [user   4.4M]  reads_2.fq.gz
`-- [user   9.0K]  reference.fasta

Run IVA with trimmomatic on the data copied to test by the automated test

[user@cn3144]$ cd test
[user@cn3144]$ iva --threads 2 --pcr_primers hiv_pcr_primers.fa \
  -f reads_1.fq.gz -r reads_2.fq.gz \
  --trimmomatic $TRIMMOJAR \
  iva.out2  

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. iva.sh), which uses the input file 'iva.in'. For example:

#! /bin/bash

function fail {
  echo >2 "$@"
  exit 1
}

module load iva/1.0.11 || fail "could not load iva module"
iva --threads $SLURM_CPUS_PER_TASK \
  -f read1.fq.gz -r read2.fq.gz \
  --trimmomatic=$TRIMMOJAR \
  sample.iva || fail "iva return non-zero exit status"

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 iva.sh

Create a swarmfile (e.g. iva.swarm). For example:

iva -r sample1_r1.fq.gz -f sample1_r2.fq.gz --trimmomatic=$TRIMMOJAR --threads $SLURM_CPUS_PER_TASK sample1_out
iva -r sample2_r1.fq.gz -f sample2_r2.fq.gz --trimmomatic=$TRIMMOJAR --threads $SLURM_CPUS_PER_TASK sample2_out
iva -r sample3_r1.fq.gz -f sample3_r2.fq.gz --trimmomatic=$TRIMMOJAR --threads $SLURM_CPUS_PER_TASK sample3_out

Submit this job using the swarm command.

swarm -f iva.swarm -g 10 -t 4 --module iva/1.0.3