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I'm excited to use it to test out some new ideas, but I had a few basic questions about using the de Bruijn graph. First, I was curious how I retrieve a de Bruijn graph node given the k-mer to which it corresponds. I looked through...the documentation, but I couldn't really find any such ability. Does the de Brujin graph in GATB support this (looking up a node by its k-mer?). Second, the release …

sequence gatb

updated 2.3 years ago • Rob

I am trying to do denovo assembly using De Bruijn Graph. What are the different ways by which I can handle/consider reverse complements reads while constructing...de Bruijn graph

next-gen Assembly genome

updated 21 months ago • kshitijtayal

Hello all I am interested in developing and analysing compacted de-bruijn graph for a number of same genes from different strains. this link (https://github.com/Malfoy/bcalm) provides a algorithm...for compacted de-bruijn graph.But I am unable to understand the input of this algorithm. Can anybody tell me other tools for same purpose

assembly

updated 6.0 years ago • sharmatina189059

Hello Everyone, I would like to know that what would be the future of De-bruijn graph based assemblers? The reason to ask this question is that already third generation sequencing technologies...are generating longer reads and De-bruijn graph technique is something which is used for assembling short reads. As longer reads are the output of sequencing...technologies the…

Assembly De Bruijn De novo

updated 7.3 years ago • saranpons3

Hi, I'm wondering if there are any existing tools for building a de Bruijn graph from raw reads? I have some doubts about current de novo assemblers, so I'd like to go to a lower level and directly...use de Bruijn graphs. But apparently there doesn't seem to be existing tools for doing this. Thanks

differential-expression graph read

updated 11.9 years ago • Tianyang Li

species. I want to assemble them to find the main genome. I have a program based on the basic de bruijn graph algorithm which is for single reads. Are there any other classic algorithm which works better in the case of...paired end reads.? (Or any other version of de bruijn graph algorithm) Also I have 3 versions of these reads from 3 sample of the same species. Could them help me to improve

RNA-Seq

updated 6.9 years ago • Star70

Hi everyone, I'm searching for a tool that can find walks in a De Bruijn graph. This can be a tool that reads an existing graph from a GFA file (or some other format), or a library. I am also interested

assembly dbsp debruijn

updated 2.1 years ago • Roman

De Bruijn graphs have become a popular of late for solving genome assembly problems. However, I'm not sure if I've ever heard "de...Bruijn" pronounced correctly--or even pronounced at all (I'm usually reading about it). As opposed to made-up programs or format...names, de Bruijn is someone's actual name from an actual culture (Dutch perhaps?), so there should be a "correct" pronunciation, am I co…

updated 10.8 years ago • Daniel Standage

Why Velvet and ABySS, the de Bruijn graph assemblers produce greater number of contigs than any other assembler? Ideally, a good assembler should generate

de novo ngs Assembly

updated 7.2 years ago • Abdul Rafay Khan

hello everebody please I am trying to assemble my reads using an algorithms for de novo assembly( De Bruijn Graph) and I don t know which algorith de novo more efficient in my case the optimal k using kmergenie

De Bruijn k-mers Assembly date palm

updated 5.9 years ago • StudentBio

plethora of tools available where you enter the read file and the software will internally build the De bruijn graph and will display the assembled genome. I want to actually see the debruijn graph that has been constructed...from the read file. Is there any tool available where you can actually view the graph from the raw-reads

next-gen Assembly genome

updated 21 months ago • kshitijtayal

I'm trying to implement a naive implementation of a de Bruijn graph. **For now I wonder how the reverse-complement sequences should be handled** ( related: https://www.biostars.org...the kmers of a read as well as its' reverse-complement kmers. But I don't think that duplicating the graph is a correct way to handle things. Here is my current javascript source . It may be just wrong. https://g…

debruijn graph javascript algorithm

updated 8.0 years ago • Pierre Lindenbaum

Hi everyone, I am trying to build De Bruijn graph from short reads. I have some reads that has length < 10 (0.01 % only). I am just worried if those reads (however very...small % of them) will create problem for graph building? **The stats i am getting for graph building is :** bank bank_uri : SRR2847…

Assembly genome sequence

updated 6.5 years ago • faraz.k89

Hello All, I would like to know that "Is De-Bruijn graph only the best approach for assembling short reads from 2nd generation sequencing technologies?" or are there...reads from 2nd generation sequencing technologies? what would be the maximum read length with which De-Bruijn graph approach will work best? Please reply and thanks in advance

Assembly genome sequencing

updated 7.3 years ago • saranpons3

From hearsay I know that de Bruijn graphs of large genomes (e.g. human) are usually constructed with k = 51, or that k = 51 is at least a good initial choice. I

de-bruijn-graph

updated 22 months ago • sebastian.schmidt.helsinki

and their usage. I know (sort of) how does the BWA works independently, and also how does the de Bruijn graphs works independently, but I do not know, when and why does the assembler softwares use which one (is this about...mapping to reference versus align de novo...? I really don't get it....). So if somebody could give me some brief explanation about the differences (usage in particular

Assembly genome alignment

updated 7.5 years ago • gerberd1990

AAACCT, should ACCT(TGGA)(forward) and TCCA(AGGT)(backward) considered also a same node in the de-Bruijn graph? Or just divided them into two seperated node

de-Bruijn graph sequence assembly

updated 6.2 years ago • 934963534

Hello All, I know that we have the following de novo assembly approaches for assembling the reads from NGS technology. Taken the list from this paper (http://ieeexplore.ieee.org...stamp/stamp.jsp?arnumber=6616523) 1) Graph based (Overlap-Layout-Consensus, De Bruijn Graph) 2) Seed Extension (Some examples: SSAKE, VCAKE) 3) String graph …

de novo Assembly

updated 7.6 years ago • saranpons3

I'm not sure I fully understood De Bruin graph when it comes to genome assembly issue. I know that assembly by De Bruin graphs is based on kmers instead of overlapping...sequences. But when the graph is done, finding the eulerian path inside (i.e., the contig) is related to the fact that reads overlap, isn't it? I mean would...it be possible to assemble non overlapping reads with a De Bruin graph

Assembly De-Bruijn-graph

updated 21 months ago • andynkili

I just made for teaching in our course on "Genome scale algorithms" at the University of Bergen. De Bruijn Graphs (DBG) are popular, among other applications, for the assembly of NGS short reads. Therefore, they have been included...demonstrating the core concepts and assembling some short sequences. Thanks to using the [igraph][2] graph analysis library, the code can be very compact and at the s…

python deBruijnGraph de_bruijn_graph assembly teaching

updated 2.1 years ago • Michael Dondrup

47-53_17-12-2018_231354 > > > [21:47:53 17/12/2018] --> Building de Bruijn graph... Graph will be > written in > kiss_results3/graph_F22merged_trimmedQ20_R1_F22merged_trimmedQ20_R2_F24merged_trimmedQ20_R1_F24merged_trimmedQ20_R2_F25merged_trimmedQ20_R1_F25merged_trimmedQ20_R2_F26merged_trimmedQ20_R1_F26merged_trimmedQ20_R2_F29mergek51

kissplice SNP RNA-Seq

updated 5.4 years ago • erica

Is there any open source java de novo assembly softwares or de bruijn graph algorithms? Thanks

differential-expression assembly

updated 11.3 years ago • lyz10302012

Hi, I was wondering if it is possible to insert further k-mers into an existing de Bruijn Graph with [GATB-core][1]? I'd like to add another sequence into a graph by iterating over the k-mers and add them to an existing...graph. Is such a functionality realized yet? If so, can one re-trigger the tip/bulge removal? Best, TK [1]: http://gatb-core.gforge.inria.fr

GATB

updated 6.8 years ago • TK

make install) I am getting an error about 3 minutes after running the above line: Building de Bruijn graph... Graph will be written in results/graph_PF01_R1_PF01_R2_k41.[edges/nodes] estimated values: nbits Bloom 33

kissplice

updated 6.2 years ago • vshiv

the short reads are broken into shorter fragments (K-mer) and then found the overlap k-mer by the de Bruijn algorithm-based assembler software for transcriptome assembly, instead of using the entire read for finding the

Assembly de Bruijn algorithm K-mer

updated 7.6 years ago • seta

lots of RAM is a requirement limits some assemblies, can zram be used to make assembly faster? Are de-bruijn graphs generally compressible? Do de novo assemblers already do compression on the graph anyway? It is trivially

assembly

updated 11.4 years ago • benjwoodcroft

MiSeq 2x250bp reads (after merging single-end 400-450bp). The genome size is ~20Mb. I think de Bruijn graph based assemblers is not the way to proceed with such dataset, isn't it? Have you had some experienced assembling

assembly miseq denovo

updated 11.3 years ago • Leszek

While going through the code of string graph assembler (SGA) and especially Heng Li's implementation of BCR algorithm for fast indexing of sequence libraries (https...that constructing Burrows Wheeler transform in SGA has many similarities with k-mer counting in de Bruijn graph-based genome assembler. In my naive understanding of BWT (but not BCR code), constructing BWT index is likely

updated 10.6 years ago • ugly.betty77

Dear All, I'm running KisSplice-2.4.0-p1, but in the first process " Building de Bruijn graph" I get the following error: kissplice -s 1 -k 41 --experimental -r ./sample_example/reads1.fa -r ./sample_example/reads2.fa...gt; [08:58:55 29/09/2018] --> Building de Bruijn graph... > Graph will be written in results/graph_reads1_reads2_k75.[edges/nodes] > Exceptio…

RNA-Seq SNP kissplice

updated 5.6 years ago • 963786304

available for upload. A summary of GATB-Core 1.3.0 new features an updates is as follows: * A new graph object is introduced: GraphUnitigs, optimized to traverse unitigs but not to query individual kmers * A few graph API

gatb next-gen

updated 11 months ago • patrick.durand

are there?) And how do I merge the nodes into a single fasta so that I can BLAST it? I got the de Bruijn graph, generated in Bandage (in red the contigs with depth above 1000): ![enter image description here][1] would it help

genome de contigs assembly spades bruijn

updated 2.5 years ago • marongiu.luigi

reads. Is there a coherent, intuitive explanation why that is so? Does the effectiveness vary among de Bruijn graph (eulerian path) methods and overlap-consensus (hamiltonian path) methods? Is there any published research that

next-gen sequencing assembly

updated 10.8 years ago • Gingi

Hi Are there existing tools for visualizing RNA-Seq splicing graphs from de novo assembly without a reference genome? What I'd like is something that can show how read goes from one exon...to another and the coverage of each exon. Are there such tools using only contigs assembled by a de novo assembler and the reads? Thanks

rna-seq splicing graph assembly

updated 8.4 years ago • Tianyang Li

Ecoli strains and I would like to perform reference-free variant calling. I would like to use the De-Bruijn graph method to go about it. Which tool would be the best to go about it? I have gone through Cortex, which I feel shall

Reference-free variant Cortex_var De-Bruijn graph calling

updated 2.3 years ago • srividhyasainath2

Which assemblers don't rely on k-mers but can also be used for large genomes eg. vertebrates?

Assembly

updated 4.4 years ago • DNAlias

www.biostars.org/u/2/), --- ### [Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2 | Genome Biology | Full Text](https://genomebiology.biomedcentral.com/articles/10.1186...6) (genomebiology.biomedcentral.com) Cuttlefish 2 is a tool for efficiently computing the compacted de Bruijn graph (or a simplitig covering of the de Bruijn graph) from either…

herald

updated 20 months ago • Biostar

a viral genome using two different assemblers e.g., Megahit and Metaspades. Both the assemblers uses de bruijn graphs but might use different k-mers because both the assemblers uses multi k-mer approach. I aligned the contigs

Assembly

updated 3.6 years ago • Rashedul Islam

on the newer version. - kallisto 0.46.1 generated index size of 2,218,101 kb [build] target de Bruijn graph has 1202693 contigs and contains 117035043 k-mers - kallisto 0.50.1 generated index size of 285,725 kb [build...target de Bruijn graph has 1013194 contigs and contains 117035043 k-mers For detail, I've used windows (intel) for using version 0.46.1

index version kallisto

updated 5 months ago • estilo

at choosing a specific k-mer size on metagenome assemblies pipelines (particularly based on de Bruijn graphs)? I have read an issue here https://github.com/ablab/spades/issues/251 where coverage seems to be a great determinant

Assembly metagenomics k-mer

updated 3.2 years ago • v.berriosfarias

Hi there, I have sequencing data from a Nanopore run which I used to create a de novo assembly using Flye. Now I want to plot the genome coverage (in %) over the run duration (hh:mm:ss). Can anyone suggest a tool...for creating such a graph? Thanks

flye Nanopore graph genome assembly

updated 14 months ago • j.zeidler

i have this code srn.scatterplot(base.conc, base.uptake, hue = base.Type) to plot a dispersion graph, but whe i try, appear this error: --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[13], line 2 1 # Gráfico de dispersão utilizando

graph dispersion seaborn

updated 12 weeks ago • brunofelicianodeomena

Hello members, I would like to know that is there any guidelines to choose K-mer size for Debruijn graph based assembly (2nd generation sequencing reads). I have F.vesca data set in which total number of reads is 12803137...Hello members, I would like to know that is there any guidelines to choose K-mer size for Debruijn graph based assembly (2nd generation sequencing reads). I have F.vesca data …

k-mer de bruijn graph

updated 6.7 years ago • saranpons3

Hi all. I'm performing GO enrichment analysis in de novo RNAseq analysis. So, I created a graph with REVIGO and outputed it in R using script exported by REVIGO. But the shape of...outputed graph was broken, and the position of value and log_size were reversed. Why do I get different output even though I use the same

GO ggplot2 Enrichment_analysis REVIGO

updated 2.6 years ago • Riku

For each starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. Mapsembler2 may be used for (not limited to): - Validate an assembled sequence (input as starter...e.g. from a de Bruijn graph assembly where read-coherence was not enforced. Checks if a known enzyme is present in a metagenomic NGS read

minia mapsembler next-gen Assembly

updated 2.5 years ago • pierre.peterlongo

I am required to assemble (de novo) the below very short 'toy' reads into contigs. If someone could recommend the best freeware for assembling via Greedy...method, Overlap Consensus-layout and/or K-mer graph (de brujin graph) it would be greatly appreciated. I have attempted to use SPAdes, however, have encountered issues due

De Brujin Greedy De Novo unpaired Freeware

updated 7.2 years ago • gs376

to change the `--timeout` parameters? Thanks in advance! [09:55:58 03/03/2018] --> Building de Bruijn graph... Graph will be written in results/graph_480_001_480_002_494_001_494_002_499_001_499_002_500_001_500_002_CW1_001_CW1_002_CW4_001_CW4_002_CW1F2_001_CW1F2_002_CW2F2_001_CW2F2_002_k41

kissplice TWAS

updated 6.2 years ago • audrahuffmeyer

Hi everyone Just looking for suggestions on which is the best tool to try build a genome graph out of alignments from many de novo assemblies? I have seen cactus used in the vg publication and see novograph as an alternative

updated 3.5 years ago • samuel.a.odonnell

to assemble and showing good coverage in the data. Is there a tool that uses the output of multiple de Bruijn Graph assemblies to identify trusted contigs that were constructed in all (or most) of the assemblies? Could using

Assembly genome

updated 4.3 years ago • lukas.hellmann

tool providing efficient data structures and algorithms to decypher NGS reads by means of kmers, de Bruijn graphs, hash tables, etc. This library has already been used to design read correctors, assemblers, SNP callers, etc

next-gen GATB

updated 13 months ago • patrick.durand

s not enough information to determine the scaffolds or is it? How a scaffold is determined in the De Bruijn graph versus a conting? How spades.py knows the insert size of the specific protocol used to sequence, or just assumes

Assembly

updated 22 months ago • elbecerrasoto

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