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Old 08-06-2013, 09:14 AM   #1
nareshvasani
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Location: NC

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Smile Velveth and velvetg.

Hello Everyone,

This is the first time I am using Velveth and velvetg.
I have around 5 million single end read, which has 50-300bp long sequences.
I used below cmd, and it work jusdt fine.
# velveth auto 31,45,2 -fastq -short -inputfile
output# it gave me 7 file with kmer length 31,33,35,36,39,41 &43.

Can anybody please give me suggestion about which kmer length to select, do i need to use long or short read in command?

How do I execute velvetg cmd?
What cutoff and min_contig_length to use?

Thanks in advance!
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Old 08-09-2013, 08:00 AM   #2
jebowers
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You need to run velvetg 7 different times to test all the different k-mer lengths

minimum contig length for most things will be at least 100 possibly more depending on what the intended use of the data is. Generally really short contigs <100 are more trouble than they are worth for most projects, although they might be useful to suggest complexities like duplications or tandem repeats in the assembly.

basically the command should be
# velvetg {file name of the 7 folders created in velvet h}

based on the number of reads it should take only a few minutes even on a desktop for each run.

Generally it is hard to tell from the information given what kmer is best in advance, generally longer is better but not always. The best kmer is generally the one that puts the most bp in the fewest contigs in the assembly results. The program makes it easy to test multiple kmers.

Coverage cutoff is really unknown depending on what your source data is, basically it depends on the expected depth of coverage. Probably not necessary to mess with it.

As for short/long it is a command for velveth and you would have to re-run that with the -long option as -short is only for illumina reads generally <200. Short may work ok but it is unclear on a 300bp read.
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Old 08-09-2013, 08:09 AM   #3
nareshvasani
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Location: NC

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Smile

Quote:
Originally Posted by jebowers View Post
You need to run velvetg 7 different times to test all the different k-mer lengths

minimum contig length for most things will be at least 100 possibly more depending on what the intended use of the data is. Generally really short contigs <100 are more trouble than they are worth for most projects, although they might be useful to suggest complexities like duplications or tandem repeats in the assembly.

basically the command should be
# velvetg {file name of the 7 folders created in velvet h}

based on the number of reads it should take only a few minutes even on a desktop for each run.

Generally it is hard to tell from the information given what kmer is best in advance, generally longer is better but not always. The best kmer is generally the one that puts the most bp in the fewest contigs in the assembly results. The program makes it easy to test multiple kmers.

Coverage cutoff is really unknown depending on what your source data is, basically it depends on the expected depth of coverage. Probably not necessary to mess with it.

As for short/long it is a command for velveth and you would have to re-run that with the -long option as -short is only for illumina reads generally <200. Short may work ok but it is unclear on a 300bp read.
Thanks Jebowers,
In velvet manual it says it doesn't matter if you select long or short option.

I really appreciate your feedback!
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