All Questions
8
questions
1
vote
0
answers
562
views
DNA genome string reconstruction from k-mer
I have the following quiz question, but the Pattern1 for both (ACC|ATA) and (CGA|ACT) are unique (just grep for ...
- 141
1
vote
1
answer
212
views
Comparing homozygosity of k-mer plots
Attached are two kmer plots from two closely related species. Is that safe to say that the one on the left has higher homozygosity than the one in the right k-mer plot, due to a low to almost flat ...
0
votes
1
answer
470
views
Understand this Kmer plot from Merqury?
The attached figure is generated based on Illumina reads from multiple individuals compared to genome assembly. Looks like there are a lot of kmers are reads only (grey colored). Also, a blue peak (2x ...
1
vote
1
answer
70
views
Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)
Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment.
Is there a way for me to do a "...
- 1,603
1
vote
1
answer
296
views
Will using smaller kmers help get larger contigs? If not, then what?
I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas.
Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
- 1,007
8
votes
2
answers
2k
views
estimate genome size: kmer-based approach from PacBio reads
Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)?
Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
- 2,706
35
votes
2
answers
3k
views
Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?
Why do some assemblers like SOAPdenovo2 or Velvet require an odd-length k-mer size for the construction of de Bruijn graph, while some other assemblers like ABySS are fine with even-length k-mers?
- 5,632
14
votes
3
answers
530
views
How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers?
In Computer Science a De Bruijn graph has (1) m^n vertices representing all possible sequences of length n over ...
- 669