ABySS want contigs < 500 pb - how to change parameter?

[Philippine De Boissel]

Hello!

I have run abyss-pe command using -s=100 because I know I should get some small contigs.

However my output shows a min of 500.

n                n:500    L50    min    N80    N50    N20    E-size    max    sum             name
2215473    2506    831    500    572    761    1277    1650    35565    2005430    MD-unitigs.fa
2214953    2545    825    500    575    774    1381    1678    35565    2074029    MD-contigs.fa
2214805    2556    824    500    576    777    1416    1687    35565    2095246    MD-scaffolds.fa

How can I change the minimum contig length, please?

Thank you!

[Ben Vandervalk]

Hi Phillipine,

You can report stats with a minimum sequence length threshold of 100 bp by running `abyss-fac -t100 <FASTA_FILE>`.

The assembly FASTA files contain all sequences >= k-mer size (k).  (It is not possible to generate sequences shorter than k with a de Bruijn graph assembly.)

- Ben

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