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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.

Assembly

Assembly is run with the script iva. An explanation of all options is here, or you might want to look at the examples (link to be added) 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)
• iva_qc_make_db - makes a database for use as input to iva_qc.