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iva examples

martinghunt edited this page Jul 9, 2015 · 5 revisions

Minimal examples

To run a de novo assembly on a set of read pairs, with forwards and reverse reads in two separate files:

iva -f reads_fwd.fastq -r reads_rev.fastq Output_directory

If instead you have a single file of interleaved paired reads:

iva --fr reads.fastq Output_directory

## Recommended usage: trim reads It is highly recommended to trim Illumina adapters and pcr primer sequences off the reads before assembling. Read trimming generally has a huge positive effect on the quality of the output. IVA trims Illumina adapters using Trimmomatic, then trims any perfect matches to PCR primers at the start of reads.

IVA is distributed with a file of Illumina adapters, but you may get better results if you know your own adapter sequences and use those instead. You need to provide your own FASTA file of primer sequences.

To turn on Trimmomatic, we need to tell IVA where the trimmomatic jar file is:

iva --trimmomatic /path/to/trimmomatic-0.32.jar --fr reads.fastq Output_directory

To also turn on PCR primer trimming:

iva --trimmomatic /path/to/trimmomatic-0.32.jar --pcr_primers primers.fasta --fr reads.fastq Output_directory

If you do have your own file of Illumina adapters:

iva --trimmomatic /path/to/trimmomatic-0.32.jar \
    --adapters adapters.fasta \
    --pcr_primers primers.fasta \
    --fr reads.fastq Output_directory

Other examples

To extend an existing FASTA file of contigs:

iva --contigs contigs.fasta --fr reads.fastq Output_directory

Input files can be gzipped - IVA will do the right thing with files that have a .gz extension:

iva --contigs contigs.fasta.gz --fr reads.fastq.gz Output_directory

Use 8 threads instead of the default 1 thread:

iva --threads 8 --fr reads.fastq Output_directory

Increase the maximum insert size from 800bp (default) to 1000bp:

iva --max_insert 1000 --fr reads.fastq Output_directory
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