Question: tool for consensus-contigs from mutiple dBG-Assembler?
0
gravatar for lukas.hellmann
5.0 years ago by
Germany
lukas.hellmann0 wrote:

Hello everyone,

I am trying to assemble a genome full of repetitive sequences. So far I tested SOAPdenovo2, platanus, (dip)SPAdes and velvet. I noticed a huge difference in the resulting contigs, not only in statistics (N50, number of contigs, etc..), but also on sequence level.

Some contigs seemed to be consistent though all assemblies though, meaning they are probably easiest to assemble and showing good coverage in the data. Is there a tool that uses the output of multiple de Bruijn Graph assemblies to identify trusted contigs that were constructed in all (or most) of the assemblies? Could using mutiple assemblers at the same time be an approach to increase the quality of genome draft?

Thank you in advance!

assembly genome • 1.5k views
ADD COMMENTlink modified 7 months ago by fabiomarcelomedvet0 • written 5.0 years ago by lukas.hellmann0
0
gravatar for lukas.hellmann
5.0 years ago by
Germany
lukas.hellmann0 wrote:

I just found what I was looking for: http://sourceforge.net/projects/metassembler/

Names of other similar tools are appreciated.

ADD COMMENTlink written 5.0 years ago by lukas.hellmann0
0
gravatar for fabiomarcelomedvet
7 months ago by
fabiomarcelomedvet0 wrote:

Hi. I've been testing METASSEMBLER, CISA, MIX, GARM, GAM-NGS. Take a look on these:

http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000400553 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1213-3

ADD COMMENTlink written 7 months ago by fabiomarcelomedvet0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2132 users visited in the last hour