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
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.
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.
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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).
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