Question: metavirome coverage with spades assembler
0
gravatar for scarabbeetle
3.1 years ago by
United States
scarabbeetle0 wrote:

Hi 

I am completely new to this field and have no experience in bioinformatics . We have recently sequenced a metavirome using illumina miseq platform (2x300). All the reads were assembled using Spades genome assembler available on illumina basespace using default settings. The output contigs had filenames  like 6048_NODE_27_LENGTH_43376_COV_6.27809_ID_53 

In this example what does LENGTH_43376_COV_6.27809 mean 

From what I understood cov indicates kmer coverage can this information be used to calculate the actual contig coverage ? 

 

Thanks 

ADD COMMENTlink modified 3 months ago by yangchengzhong5180 • written 3.1 years ago by scarabbeetle0

Is the lenght of this particular contig 6,909 bp?

ADD REPLYlink written 3.1 years ago by 5heikki7.7k

Hi, I am encountering the same problem? I want to know whether you soved the problem. If yes, could you please tell me how?

ADD REPLYlink written 3 months ago by yangchengzhong5180
0
gravatar for Sej Modha
3 months ago by
Sej Modha3.7k
Glasgow, UK
Sej Modha3.7k wrote:

SPAdes employs Velvet assembler headers style explained in details on

http://seqanswers.com/forums/showthread.php?t=6887 and Confusion about the kmer coverage

ADD COMMENTlink modified 3 months ago • written 3 months ago by Sej Modha3.7k
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