![](images/graphics/blank.gif)
Bruijn graph
-
Continued part 1, part 2 of ebook "Coding theory and applications" provides readers with content including: on extendibility of additive code isometries; the extension theorem with respect to symmetrized weight compositions; minimal realizations of syndrome formers of a special class of 2D codes; shifted de bruijn graphs; new examples of non-abelian group codes; cyclic convolutional codes over separable extensions; reachability of random linear systems over finite fields;...
180p
dieptieuung
19-07-2023
8
4
Download
-
Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions.
12p
vialfrednobel
29-01-2022
13
0
Download
-
Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number.
24p
viarchimedes
26-01-2022
7
0
Download
-
The challenges when developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize a de Bruijn graph, with which complexity grows linearly with data size while suffering from errors and repeats.
20p
vitzuyu2711
29-09-2021
12
1
Download
-
A popular strategy to study alternative splicing in non-model organisms starts from sequencing the entire transcriptome, then assembling the reads by using de novo transcriptome assembly algorithms to obtain predicted transcripts.
14p
visilicon2711
20-08-2021
7
1
Download
-
The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection.
12p
viwyoming2711
16-12-2020
16
1
Download
-
Processing of reads from high throughput sequencing is often done in terms of edges in the de Bruijn graph representing all k-mers from the reads. The memory requirements for storing all k-mers in a lookup table can be demanding, even after removal of read errors, but can be alleviated by using a memory efficient data structure.
19p
viwyoming2711
16-12-2020
15
0
Download
-
Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip method.
14p
vikentucky2711
24-11-2020
7
1
Download
-
Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers.
13p
vikentucky2711
24-11-2020
13
1
Download
-
Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs.
12p
vioklahoma2711
19-11-2020
6
1
Download
-
The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other assembly methods.
9p
viflorida2711
30-10-2020
12
2
Download
-
De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph.
15p
viconnecticut2711
29-10-2020
9
1
Download
-
Many organisms, in particular bacteria, contain repetitive DNA fragments called tandem repeats. These structures are restored by DNA assemblers by mapping paired-end tags to unitigs, estimating the distance between them and filling the gap with the specified DNA motif, which could be repeated many times.
10p
viconnecticut2711
28-10-2020
10
0
Download
-
Aligning short reads to a reference genome is an important task in many genome analysis pipelines. This task is computationally more complex when the reference genome is provided in the form of a de Bruijn graph instead of a linear sequence string.
10p
viconnecticut2711
28-10-2020
15
1
Download
-
Several standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-the-art assemblers often did not benefit from this pre-correction step.
13p
vijisoo2711
27-10-2020
15
1
Download
CHỦ ĐỀ BẠN MUỐN TÌM
![](images/graphics/blank.gif)