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
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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