I have done my de novo assembly using ABySS. I am expecting small contigs but abyss-pe has a default parameter: min length of 500. How can I change that to 200 pb, please?
Are you sure ABYSS has this default contig size? I couldn't find it either on the docs, or online discussions, and I think there is no such default - I could be wrong, though.
There are several online discussions about contig size related to abyss-fac, the tool used to calculate assembly contiguity statistics. This tool indeed has a default of excluding from the computation contigs shorter than 500bp, and you can include shorter contigs by using the parameter -t 200 or --min-length=200.
That is exactly right, @h.mon. The 500 bp length threshold is only used by abyss-fac when calculating contiguity stats (e.g. N50). (abyss-fac has a -t option for changing the threshold, which defaults to 500 bp.)
The output assembly FASTA files from ABySS are never filtered by sequence length. The minimum sequence length will be generated will be the k-mer size, as per the de Bruijn graph assembly method.