gsAssembler - predicted genome size?

[Jordy224]

Hello a I have a quick question concerning "newbler" gsassembler(v2.3). Can anyone suggest how to find the predicted genome size from the output of a de novo assembly?

To calc the n50 stat the predicted genome size is required, so I assume its there somewhere...

Thanks in advance,

Jordy

[RCJK]

Hi Jordy,

Look in the "454NewblerMetrics.txt" file. It lists the estimated genome size as well as the N50 Contig size (but I'm not sure if this is for all contigs or only large contigs).

[flxlex]

To calc the n50 stat the predicted genome size is required, so I assume its there somewhere...Jordy

Interesting that you write this, because the N50 definition variably is relative to estimated genome size, reference genome size (for reference assisted assembly/mapping) OR total assembled size. It is the last definition newbler uses: smallest contig size such that half the assembled bases are in contigs of at least that size.

Obviously, the N50 size is also dependent on the minimum contig length included in the total, which in case of newbler is 500 bp.