Talk:Sequence assembly

message: De-novo application is not in the list  —Preceding unsigned comment added by 130.225.211.21 (talk) 10:29, 2 September 2009 (UTC)
thread_title:  ALLPATHS 

message: a column that denotes support for paired end data.  —Preceding unsigned comment added by 130.225.211.21 (talk) 12:14, 2 September 2009 (UTC)
thread_title:  Add to assembler table 

message: What's with the algorithm?  Surely, it would be more relevant to give the optimal (NP-complete) algorithm - than a very simplistic one?
: The assembly problem is a variation of Hamiltonian path problem which is known to be NP-hard in its function problem version known as Travelling salesman problem. The use of heuristic is then justified. However I think that pseudocode should be placed elswehere i.e. in the Shortest common supersequence article.
: 213.121.151.178 03:37, 26 February 2006 (UTC)
thread_title:  Algorithm? 

message: I'm not happy with this.  Naively comparing the fragments of size n to a genome of size m is O(nm), so not much better than O(n^2) for de novo.  The O(log n) seems ridiculous and should probably be O(n log n), but still needs a cite.  —Preceding unsigned comment added by Ketil (talk • contribs) 09:14, 26 February 2009 (UTC)
replies: text: A lookup against a fixed set of sequences (like a genome) can be trimmed down to take a maximum of O(n) by using hashing techniques, running on real world data it's even closer to O(1). The paper on "SSAHA" gives quite a nice introduction. Extending the approach to the comparison of one set of sequences against (another or the same) set of sequences then adds an additional layer of complexity, but it's closer to O(log n) than O(n log n). However, papers citing the complexity of the overlapper algorithms are hard to come by, the authors normally don't go that deep into the details. BaChev (talk) 22:38, 27 February 2009 (UTC)
thread_title:  Complexity of de novo vs mapping assembly 

message: Do any frameworks exists that challenge various assemblers to perform the same assembly and then score their results? --Jhannah (talk) 09:36, 17 April 2009 (UTC)
thread_title:  Comparative scoring framework? 

message: What the hell does "C++" in the ALLPATHS-LG entry mean?  —Preceding unsigned comment added by 162.129.251.17 (talk) 17:55, 3 May 2011 (UTC)
thread_title:  Licenses 

message: Can we add some? --Dan Bolser (talk) 03:57, 14 September 2012 (UTC)
thread_title:  Pictures and figures? 

message: This list is rather long - perhaps this section should be renamed 'Notable assemblers', and assemblers without their own article removed. Any thoughts on this? Amkilpatrick (talk) 17:59, 28 June 2017 (UTC)
replies: text: I've been bold and cut this list back with this edit Amkilpatrick (talk) 11:03, 6 July 2017 (UTC)
replies: text:  You are treading a very, very fine line here. Who decides what is 'notable'? You? On what criteria: used today, number of citations, number of genomes assembled with them, availability, known by you, own pages in Wikipedia? None of these are good measures. E.g., Euler was the first assembler demonstrating feasibility of kmer (de-Bruijn Graph) assembly, is that not notable? The Staden assembler and Celera assemblers were used for assembly of the human genome, parts of WGA continue to live nowaday in Canu for long read assembly, not notable? Etc.pp for quite a number of assemblers which were on that list. I do agree that this article has its problems and should be revised, maybe by describing how the assembly problem evolved over time and leading to several approaches (overlap, kmer, etc.) for different sequencing types which all behave differently (Sanger, 454, Illumina, PacBio & ONT) and using all kind of tricks (ranging from massive parallelisation to data reduction like bloom filters etc). Simply culling the list is not helpful. BaChev (talk) 12:54, 19 July 2017 (UTC)
replies: text: As I mentioned, the criteria for 'notability' was their own articles in WP. I agree it's not a perfect measure, but I was basing this on the guidelines at WP:CSC, ie, every entry has its own article, or no entry has its own article. I take your point that the list is now maybe too short, but the list of dozens that was there before was equally unhelpful. There is definitely scope for expanding the article with the description you suggested though, perhaps Sequence assembly#Influence of technological changes or a history section would be suitable? Amkilpatrick (talk) 13:37, 19 July 2017 (UTC)
replies: text:  WP:CSC has a third category: "Short, complete lists of every item that is verifiably a member of the group." That list is probably still in the 32k boundary proposed. Whatever you do when pruning the list, be prepared to eventually have 'interesting' reactions. If you go back in time for this article you will see an edit war happened when someone tried to push his product in the then list by removing almost everything except that one product and a few fig leaf excuse entries. The current list was a way out of that. BaChev (talk) 16:22, 19 July 2017 (UTC)
thread_title:  'Available assemblers' list 

message: I was a bit confused about the section entitled De-novo vs. mapping assembly. It's my understanding that read mapping isn't an assembly technique, but rather something different. I think this article gives some indication of the difference between mapping and assembly. Mapping will only give you an idea of how your organism's genome sequence differs from that of another organism, and will miss any parts of the genome not present in the reference. I think it would be more appropriate to rename this section "De novo assembly vs read mapping", and use it to explain the difference between these two ways to compare the DNA of organisms, rather than referring to them as two methods of assembly. 
Happy to discuss the terminology issue here, but if I don't hear back soon I will go ahead and make the edit.
Maonao (talk) 08:57, 18 October 2017 (UTC)
thread_title:  Mapping assemblies 

message: — Assignment last updated by Tmmyn (talk) 05:15, 14 October 2022 (UTC)
thread_title: Wiki Education assignment: Bioinformatics