Question: After assembly with Falcon
gravatar for alexis.groppi
3.1 years ago by
France/Bordeaux/University of Bordeaux
alexis.groppi30 wrote:


I'm working on a vegetal diploid genome (aroud 200 Mb) trying to obtain the best assembly with PacBIO RSII P6-C4 reads (70X coverage).

I have used Falcon and Falcon Unzip (0.7+git.2059148090374ac08a494d842dc1def105aeee50) Then I have run fc_quiver from this Falcon 0.7

I have now a "phased" assembly consisting in two files : cns_p_ctg.fasta (primary contigs) and cns_h_ctg.fasta (haplotigs) After this step, I thinks that it is a good choice to do an additional polishing with Arrow from (smrtlink/ Is this OK ?

But then I'm a bit confused. The final assembly is ONLY cns_p_ctg.fasta (primary contigs) ? or Should I merge cns_p_ctg.fasta (primary contigs) and cns_h_ctg.fasta (haplotigs) ?

I have read and heard so many diffrent things about this strategy ...

My opinion is that the final assembly would be only the primary contigs and the haplotigs (cns_h_ctg) are useful to determine the differents alleles in the diploid genome.

Am I right or completly wrong ?


pacbio assembly genome • 1.3k views
ADD COMMENTlink written 3.1 years ago by alexis.groppi30

I would say you're right. Given that you try to assemble a diploid heterozygous genome.

The final assembly would only consist of the primary contigs. In an homozygous (diploid) assembly you would also only result in a single haplotype. The other haplotigs are indeed to determine the different allelic variation.

ADD REPLYlink written 3.1 years ago by lieven.sterck10k

Thank you for confirming my opinion and removing my doubts ;)

ADD REPLYlink written 3.1 years ago by alexis.groppi30
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