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Old 01-18-2018, 05:59 AM   #1
hetappi
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Location: Cologne, Germany

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Default Combining PacBio assembly with 10X assembly?

Dear all,
Currently we created an assembly of a highly repetitive plant genome with
60x coverage of Pacbio reads (assembler HGAP4).

In addition we have 100x coverage with 10X Illumina reads. These were
assembled using the supernova assembler.

Has anyone ideas how we could combine these two assemblies? The genome
size is about 2Gbases.

any help appreciated

hetappi
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Old 01-19-2018, 02:48 AM   #2
hetappi
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Now I used the program scaffold_builder, see
https://sourceforge.net/projects/scaffold-b/

This program did run for a few days and then it produced
a SINGLE CONTIG of 2GigaBases. I am a little bit in doubt about
this fabulous result.
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Old 09-20-2018, 04:47 AM   #3
horvathdp
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Hi, did you eventually come to a good conclusion with your study? I have a similar situation, and would love to know what worked for you.
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10x genomics, assembly, hybrid assembly, pacific biosciences

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