Question: Pacbio assembler for mid genome ?
1
gravatar for Picasa
3.3 years ago by
Picasa460
Picasa460 wrote:

Hello,

Does HGAP is efficient for assembling Pacbio reads of an estimate genome size of 700 MB ?

Where can I find benchmark test for pac bio assembler, such as how much memory required for a pac bio de novo assembly etc. ??

cpu ram • 1.1k views
ADD COMMENTlink written 3.3 years ago by Picasa460
2

Here is a link for wiki from PacBio for this topic.
You would want to consider this recommendation from PacBio.

We recommend PacBio-only de novo assembly when it is possible to get at least 50X PacBio coverage.

Recently gorilla genome was assembled using PacBio reads, so in theory it is possible to do much larger genomes (provided you have enough coverage).

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax70k
1

Do you have any clue about how much RAM we need for this kinkd of assembly ?

ADD REPLYlink written 3.3 years ago by Picasa460
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