Question: scaffolds and contigs SPADES
4
gravatar for ndp
5.1 years ago by
ndp40
United States
ndp40 wrote:

Hi, Can anybody tell me how contigs and scaffolds from SPADEs differ?  Mine appear to be identical and even in the GAGE-B study they are identical.  Other assemblers produce scaffolds with higher N50s, but SPADES doesn't.  Are they the same? Thanks! NP

 

 

 

 

scaffolds spades • 5.7k views
ADD COMMENTlink modified 5.1 years ago by anton40 • written 5.1 years ago by ndp40
2
gravatar for anton
5.1 years ago by
anton40
United States
anton40 wrote:

It's perfectly ok that scaffolds coincide with contigs in case of single paired-end library - the assembler may simply resolve almost all short repeats and thus there is nothing to scaffold.

ADD COMMENTlink written 5.1 years ago by anton40
1
gravatar for rtliu
5.1 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

If no mate-pair libraries is used, aka, use paired end reads only,  then contigs might be identical to scaffolds.

If --sc flag is used for paired end reads, then scaffolds N50 is usually higher than contigs N50.


 

ADD COMMENTlink written 5.1 years ago by rtliu2.0k

The problem is that other tools show different N50 for contigs/scaffolds. Moreover those libraries from GAGE-B appear to be paired-end. Btw in the original paper the tables show different values for contigs vs scaffolds (http://bioinformatics.oxfordjournals.org/content/29/14/1718/T4.expansion.html).

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by mikhail.shugay3.4k

Thanks for your email! I know the values are different in the GAGE-B study, but they are only slightly different whereas for most of the other tools the N50 for the scaffolds is much bigger (which is what you would intuitively expect and is the whole point of scaffolding). In this case I don't see any reason to use the scaffolds but I just want to make sure I'm not missing something since this is a new field for me.

Nicole

ADD REPLYlink written 5.1 years ago by ndp40
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