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Old 09-27-2017, 06:42 PM   #1
GUZUMO
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Default parameter 'seed kmer' of IDBA_ud

I just don't know what's the meaning of it.
Is there anyone explain it for me ?
Thanks !XD
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Old 09-28-2017, 10:00 AM   #2
Brian Bushnell
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I am not sure about IDBA, but Tadpole has a seed kmer flag, and the meaning is:

Contigs are built starting with a single kmer, then extending it. However, only kmers with a sufficiently high count (number of times they are observed in reads) are used as seeds, because kmers with a very low count are likely to be erroneous. So Tadpole's default "mincountseed=3" ensures that no contig will ever be created that does not have at least one kmer in it with a depth of at least 3. I suspect IDBA uses a similar mechanism.
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Old 10-02-2017, 06:44 PM   #3
GUZUMO
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Quote:
Originally Posted by Brian Bushnell View Post
I am not sure about IDBA, but Tadpole has a seed kmer flag, and the meaning is:

Contigs are built starting with a single kmer, then extending it. However, only kmers with a sufficiently high count (number of times they are observed in reads) are used as seeds, because kmers with a very low count are likely to be erroneous. So Tadpole's default "mincountseed=3" ensures that no contig will ever be created that does not have at least one kmer in it with a depth of at least 3. I suspect IDBA uses a similar mechanism.
Thank you .
But as idba_ud has a parameter '--min count' with description 'minimum multiplicity for filtering k-mer when building the graph', I guess maybe what you say is something like this.[?]
Sorry that I forgot to write down the description of seed kmer, 'seed kmer size for alignment'。 But I really can't understand. Is it means when constructing the graph, the first kmer needs to be this size[seed kmer] and other kmers' length will be the sum of mink and step?
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Old 10-03-2017, 02:43 PM   #4
Brian Bushnell
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Oh... in that case, speculation again, but it sounds like it is for a scaffolding phase; essentially, a match of at least that long is required in a read to consider it as having come from that scaffold.
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