Evaluate other assemblers

We've had reasonably good results with IVA, but it has a few problems:

1. Some samples are very slow, even taking multiple days. Random primers seem to be slow.
2. We find contigs with a lot of repeats, possibly caused by primer dimers. That may or may not be a problem with the assembler.
3. The IVA project is not really maintained anymore, so it may be wiser to find another tool.

A brief search for alternatives turned up SPAdes, as mentioned in an article by Sutton, as well as tadpole, mentioned in a discussion forum.

An interesting sample for experimenting on is D62201-HCV_S3 from the 26 Feb 2016.M04401 run. It looks like a mixed HCV infection with two or possibly three strains to assemble.

Edit: To Do List

• Investigate where IVA is struggling.
• Try Spades.
• Try Abyss.
• Use ntJoin to scaffold the contigs to a reference genome.
• Create a pessimistic mode for IVA for a quick attempt at assembly.
• Improve IVA's pessimistic mode by making it use the filtered reads in each step.
• Update to latest IVA fixes.
• Try Velvet.
• Optimise Velvet's input parameters / automate the determination of the parameters for each sample.
• Try Haploflow.
• Use contig merging and scaffolding to improve Haploflow's assembly results.
• Improve RP results for Haploflow.
• Compare IVA and Haploflow quantitatively.