Assembly test data

Assembly test data

The installation of IVA can be tested on a small HIV data set that is included with IVA. When run in test mode, IVA takes a copy of all relevant data into the user-specified output directory and runs an assembly. All other options are ignored, except that --threads and --trimmomatic can be used.

Without Trimmomatic

The command to run is

iva --test outdir

It will take a few minutes to run (use --threads X, where X>1 to speed it up). The output should look similar to this:

Running iva in test mode...
Copied input test files into here: /path/to/outdir/
Current working directory: /path/to/outdir/
Running iva on the test data with the command:
/bin/iva --threads 1 --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: /path/to/outdir/iva.out/contigs.fasta

The final contigs file should be in two contigs, and similar (but may not be exactly the same as) the file

/path/to/outdir/iva_contigs_no_trimmomatic.fasta

With Trimmomatic

You will need to have the Trimmomatic java .jar file. The command to run is

iva --test --trimmomatic /path/to/trimmomatic.jar outdir

The test assembly run is the same as above, except the reads will be trimmed with Trimmomatic before assembly. This produces a better assembly, with just one contig in the final output file

/path/to/outdir/iva.out/contigs.fasta

that should be similar (but may not be exactly the same as) the file

/path/to/outdir/iva_contigs_with_trimmomatic.fasta