Abyss N:500 value

Question

[wangzz.email]

HI Abyss developers,

I found that the N:500 in the Abyss-stat file is different from what I calculated. I am wondering if there is any other filtering parameters for contigs other than the length?

Thanks.

George

Answer 1

[benv]

Cross-posting Shaun Jackman's response from the ABySS Google group:

Hi, George. abyss-fac does not count Ns toward the 500 bp, and samtools faidx counts all symbols. I've added you question to the FAQ. https://github.com/bcgsc/abyss/wiki/ABySS-Users-FAQ

Cheers, Shaun