Abyss N:500 value

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

abyss assembly

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updated 10.2 years ago by benv

• written 10.2 years ago by wangzz.email •

1 answer

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

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written 10.2 years ago by benv

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