Assembly (velvet) of mate-pair data from Illumina

[Protaeus]

Hello,

I asked a similar question previously, but wanted to re-post to more specifically address the question of assembly (with velvet) rather than alignment.

I was writing to ask a question of those who have, seemingly successfully, assembled to fastq's with Illumina mate pair data. I have seen other threads in which people mention that reverse complementing the reads is a necessary prerequisite to ensure the reads are facing the correct direction. Is this true? If so, is there a tool that someone could recommend to easily reverse complement a fastq or sequence.txt file?

If you have any other suggestions for dealing with mate pair data and have suggestions of tools to accomplish those tasks, I'd greatly appreciate it.

Cheers,
John

[natstreet]

There are a number of options for reversing the reads but I prefer to use the fastx toolkit as it's the fastest option. I also like biopython and you can look into the biopython tutorial for examples.

From my own data, the biggest headache with mp data is the contamination of long inserts with short inserts, which are in the opposite read orientation. I haven't seen a good solution yet as to how to handle this. I have a somewhat related species that I can use as a reference to initially map the reads and extract those pairs that are correctly mp or short insert contamination but this has its own issues such as assuming that there are no rearrangements etc. It also still leaves most reads unmapped.

[Kasycas]

Dear natstreet,

I'm currently wondering if this is a problem I'm having as my mate pair Illumina data is not assembling as all with Velvet, although soapdenovo seems to be working ok. Why would you get short insert contamination in a materpair library ?