Using SSPACE: how to calculate 'expected/observed insert size between paired reads and the minimum allowed error?'

Question

[freuv]

Hi,

I am using SSPACE for scaffolding of AbySS contigs -- the tool requires a text library file with some info re: the reads.

It is unclear what and how the following required numbers for this text library file are calculated.

• expected/observed insert size between paired reads
• minimum allowed error

Any guidance would be appreciated. Thanks!

F

[GenoMax]

You can calculate the insert sizes using BBMap (C: Target fragment size versus final insert size ). Adjust value of k= depending size of your reads.

[freuv]

If you don't mind, can you please explain what these two values mean?

• expected/observed insert size between paired reads
• minimum allowed error

My raw reads are 150bp -- what value of 'k' would I use?

Thanks for your help!

[GenoMax]

I don't know the full context of this question so here goes. Expected insert size is something you will have determined during your library prep/QC (using e.g. bioanalyzer etc). Observed insert size is what you will get from bbmap.sh or bbmerge.sh method. This would be the reality present in your library. In general, smaller inserts cluster more efficiently on Illumina flowcells, so unless you are very careful about restricting them you will see insert sizes smaller than you expect to see. Take a look at the bbmerge guide here.