Combining PacBio assembly with 10X assembly?

hetappi · 01-18-2018, 05:59 AM

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

hetappi · 01-19-2018, 02:48 AM

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.

horvathdp · 09-20-2018, 04:47 AM

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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01-18-2018, 05:59 AM	#1
hetappi Junior Member Location: Cologne, Germany Join Date: Feb 2011 Posts: 8	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

01-19-2018, 02:48 AM	#2
hetappi Junior Member Location: Cologne, Germany Join Date: Feb 2011 Posts: 8	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.

09-20-2018, 04:47 AM	#3
horvathdp Member Location: Fargo Join Date: Dec 2011 Posts: 66	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.