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6 votes
Accepted

How the genome assembly be done after k-mer counting?

There are multiple ways of doing genome assembly. The term you are probably looking for is "De Bruijn-Graph based assembly". Using this you can find a lot more different explanations of how it is done....
skymningen's user avatar
  • 1,961
6 votes

What does it mean to collapse heterozygous alleles?

I suspect this means that either the multiple alleles are represented with an ambiguity code: Haplotype1: ATCG Haplotype2: ACCG Consensus: AYCG Or,...
Darlingtonia's user avatar
  • 2,659
4 votes
Accepted

Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?

Maximillian provided some good information, but I thought I'd add some practical considerations: All of the long-read sequencing platforms provide quite contiguous assemblies (scaffold N50s up to ...
Kieran O'Neill's user avatar
3 votes

Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?

Update: Answer was transferred to Kieran O'Neill's response, which I think is appropriate. I am not completely convinced that these technologies are necessary, but I am also not as familiar with them. ...
Maximilian Press's user avatar
3 votes
Accepted

Polymerase Cycle Assembly (PCA) is not working (Only primrs in EF Gel)

I suspect mispriming due to annealing temp being too low compared to predicted melting temp of overlap regions. As the protocol in your link notes: (3) Choose annealing temperature wisely. We ...
Armand's user avatar
  • 1,721
3 votes
Accepted

Are there known genome sequencing issues in E. coli?

Generally, gaps in genomes occur due to failure of de novo assembly -- the DNA can be sequenced accurately, but cannot subsequently be placed into a contiguous assembly due to alignment ambiguity with ...
acvill's user avatar
  • 8,296
2 votes
Accepted

How do we know which Eulerian path corresponds to the DNA sequence?

If the DNA sequence contains repetative elements, and your reads are not long enough to resolve them, you won't know if you have the right path. Usually you split your results into contiguous regions ...
swbarnes2's user avatar
  • 5,230
2 votes

Are there known genome sequencing issues in E. coli?

Summary The publication of the first complete DNA sequence of Escherichia coli was for strain K-12 substr. MG1655 in 1997. Because of historical limitations in the technology used (rather than ...
David's user avatar
  • 26.2k
2 votes

What are primary reasons for the failure to localise/anchor sequences in genome assemblies?

I'm going to re-interpret this question slightly to make it easier to answer: "Why do genome assemblies frequently consist of large numbers of short contigs rather than a relatively small number of ...
Maximilian Press's user avatar
1 vote

What is limiting the accuracy of genome sequencing today?

One that isn't on your list: cost. In the form of Oxford Nanopore data, we have extremely long reads of low accuracy. These are not too expensive but on their own they are probably not viable for ...
Maximilian Press's user avatar
1 vote
Accepted

What is the difference between contig- and read-based sequence alignment?

I have never heard the term “contig based alignment”, and your question is the only Google hit of this exact query (apart from a 2012 patent application). That said, and without knowing the exact ...
Konrad Rudolph's user avatar
1 vote
Accepted

What is known about the coding sequence of Factor H in the human genome?

As clearly stated in the WP article: The molecule is made up of 20 complement control protein (CCP) modules (also referred to as Short Consensus Repeats or sushi domains) connected to one another ...
Alan Boyd's user avatar
  • 22.8k
1 vote

What is the difference between sequence alignment and sequence assembly?

The two tasks are quite different. Aligning means comparing sequences to find differences between them. Assembling means that you take a bunch of short sequences and try to stitch them back together ...
IceCold's user avatar
  • 113
1 vote

Assembly reconciliation

This is an old question but it seems relevant to answer now given current state of art. See also this related thread on biostars. There are now many tools that perform this function, which is somewhat ...
Maximilian Press's user avatar

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