Newbler assembly - excluding specific reads?

JonB · 01-20-2010, 12:30 PM

Hi,

I have sequenced genomic DNA from a eukaryote and have ran a newbler assembly of the sff file from the 454 lab. Some of the contigs are clearly belonging together, but are not assembled into one. This seems to be caused by a few reads that looks like artefacts from the genomic amplification. (These reads are split into two and the two halves match each end of the contig, like a circle.)

I wonder if it is possible to run newbler and to specify that these reads (i have the names) should not be considered?

Thanks!

Jon

kmcarr · 01-20-2010, 02:35 PM

Jon,

Yes, you can exclude specific reads from the assembly. Create a text file with the read names you wish to exclude, one name per line, nothing else. When you run newbler use the parameter '-fe <filename>' where filename is the file described above.

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01-20-2010, 12:30 PM	#1
JonB Member Location: Norway Join Date: Jan 2010 Posts: 83	Newbler assembly - excluding specific reads? Hi, I have sequenced genomic DNA from a eukaryote and have ran a newbler assembly of the sff file from the 454 lab. Some of the contigs are clearly belonging together, but are not assembled into one. This seems to be caused by a few reads that looks like artefacts from the genomic amplification. (These reads are split into two and the two halves match each end of the contig, like a circle.) I wonder if it is possible to run newbler and to specify that these reads (i have the names) should not be considered? Thanks! Jon

01-20-2010, 02:35 PM	#2
kmcarr Senior Member Location: USA, Midwest Join Date: May 2008 Posts: 1,178	Jon, Yes, you can exclude specific reads from the assembly. Create a text file with the read names you wish to exclude, one name per line, nothing else. When you run newbler use the parameter '-fe <filename>' where filename is the file described above.