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Old 02-25-2012, 07:50 PM   #1
zhongj
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Location: Beijing

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Smile Beg for latest version of SOAPdenovo correction tool before assembly

Hi guys,
In AllPath-LG paper, “High-quality draft assemblies of mammalian genomes from massively parallel sequence data”, supplemental information, page4, it mentions
“Next read correction was done on the fragment pair reads in two steps via the modules KmerFreq and Corrector. The SOAP authors provided new error correction code along with the exact parameters to use:”
kmer_freq_pfile reads.in -k 17 -f 1 -t 48 -p mouse
correct_error_pread mouse.freq.gz reads.in -k 17 -x 8 -r 50 -l
10 -c 5 -p mouse -f 1 -j 1 -t 48

But on the BGI official web, there is only version 1.00 which was published in 2009. I had tried to mail to [email protected], but never succeed. Could SOAP authors or anyone kindly send the latest version of error correction tool to me? My email is [email protected], thank you very much!

BTW, I have a question about error correction tool version 1.00, about Corrector module:
-k [int] start of kmer frequence cutoff [default 5]
-e [int] end of kmer frequence cutoff [default 5]
Does “start of kmer frequence cutoff [default 5]” means low frequency (<5) 17 mers were edited to the closely similar high-frequency 17- mers? What does “end of kmer frequence cutoff [default 5]” means?

Thanks in advance!
Best,
Josh
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Old 02-26-2012, 01:57 AM   #2
Bukowski
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Perhaps they were referring to the 1.05 release in Feb 2011 rather than the 1.04 release that was released in December 2009?
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Old 02-26-2012, 06:56 PM   #3
zhongj
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Smile

Thank you for your reply. I mean the additional reads Correction module, rathaer than SOAPdenovo software. I have SOAPdenovo 1.05 version alredy.

Quote:
Originally Posted by Bukowski View Post
Perhaps they were referring to the 1.05 release in Feb 2011 rather than the 1.04 release that was released in December 2009?
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