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.
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.
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_qcare 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.