No Contig Cutoff?

[IWasBorg]

My resulting assembly has quite a few (80 of 180) contigs that are smaller than 1000bp, is there an option to only keep contigs above specified length on IDBA like Velvet and SPADES?

Also, IDBA happens to output scaffold.fa and contigs.fa, are there any differences between those even if using IDBA-UD? Thanks

[jvollme]

Scaffolds are sequences where several contigs are linked in a known order, but the exact sequence between them is unknown.this is possible if you have paired end sequences from a fragment library with fragments larger than twice the read size. The unknown bit is then represented by "N"s. In the contigs.fa such scaffolds would be broken down into multiple contigs.

[jvollme]

It should, however, be possible that the scaffolds file and the contigs file are identical (if there where no scaffolds). You can check by using the Unix command "diff" or by grepping for stretches of "N"s (only found in scaffolds)