What insert size for velveth (1.2.10) with 2 sets of reads with diff. insert sizes?

[Genomics101]

Greetings. I'd like to do a de novo assembly using Velvet 1.2.10 from reads of two different Illumina , one with 50 basepair reads and a 115bp insert, one with 250bp reads and 550bp insert. For velveth, how what insert size do I give it? An average? Pick the larger one? Thanks!

[mastal]

you can use both.

the 2 sets of reads will be flagged as -shortPaired and -shortPaired2, respectively, when you run velveth, and the insert lengths can be
specified using the parameters -ins_length, -ins_length_sd, -ins_length2 and
-ins_length2_sd when you run velvetg.

[Genomics101]

@mastal, thanks! I actually specified the 250bp reads as -longPaired. Do you think that was unwise?

[ctseto]

From the velvet manual:

5.6 What’s long and what’s short?
Velvet was pretty much designed with micro-reads (e.g. Illumina) as short and
short to long reads (e.g. 454 and capillary) as long. Reference sequences can
also be thrown in as long.
That being said, there is no necessary distinction between the types of reads.
The only constraint is that a short read be shorter than 32kb. The real difference
is the amount of data Velvet keeps on each read. Short reads are presumably
too short to resolve many repeats, so only a minimal amount of information is
kept. On the contrary, long reads are tracked in detail through the graph.
This means that whatever you call your reads, you should be able to obtain
the same initial assembly. The differences will appear as you are trying to resolve
repeats, as long reads can be followed through the graph. On the other hand,
long reads cost more memory. It is therefore perfectly fine to store Sanger reads
as “short” if necessary.

[Genomics101]

Thanks, ctseto, indeed I puzzled over that section for a while in making the decision