Question: Non-de bruijn graph assemblers
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gravatar for DNAlias
8 months ago by
DNAlias0
DNAlias0 wrote:

Which assemblers don't rely on k-mers but can also be used for large genomes eg. vertebrates?

assembly • 165 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by DNAlias0

Could you maybe elaborate what kind of data you're using? E.g., if you're using Illumina short reads using a non deBruijn assembler doesn't make much sense. If you're using PacBio/Nanopore data, though, then have a look into Flye, Canu, or HGAP.

ADD REPLYlink written 8 months ago by cschu1812.5k

Masurca uses both, so might be interesting:

From the website https://github.com/alekseyzimin/masurca "The MaSuRCA assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly"

Celera Assembler (precursor to Canu) was overlap consensus to my knowledge.

More than a few OLC assemblers have been created, but many are not applicable to large genomes because of memory requirements (if you're talking short reads). Long reads are a different ballgame.

ADD REPLYlink written 8 months ago by colindaven2.3k
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