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martinghunt edited this page Oct 28, 2015 · 5 revisions

IVA - Iterative Virus Assembler

IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth.

IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence.

Installation

Please see the IVA homepage for installation instructions.

The installation of IVA can be tested by running an assembly on the test data set that is included with IVA.

Assembly

Assembly is run with the script iva. An explanation of all options is here, or you might want to look at the examples first.

Assembly QC

There are two scripts for QC:

  • iva_qc - compares an assembly against a reference (or can choose the reference from a database). There is a page of options and also examples. The output files of iva_qc are explained here and the stats it makes are explained here.

  • iva_qc_make_db - makes a database for use as input to iva_qc. See this page for more help.

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