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metavirome coverage with spades assembler

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

assembly next-gen-sequencing alignment
• 2,869 views • link
updated by Ram Ram • written by scarabbeetle • scarabbeetle

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

• 0 views • link
updated by Ram Ram • written by 5heikki 5heikki

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

• 1 views • link
written by yangchengzhong518 • yangchengzhong518

1 answer

SPAdes employs Velvet assembler headers style explained in details on

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

• 1 views • link
written by Sej Modha Sej Modha

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