Questions tagged [sequence-assembly]

Sequence assembly is the process of reconstructing a DNA sequence by aligning and merging sequencing reads.

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What does it mean to collapse heterozygous alleles?

I am a bioinformatics rookie. I read a paper, it said: existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-...
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Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?

Any comparable alternatives to linked read sequencing? I read that 10X Genomics discontinued its linked-reads technologies: Discontinuation of Linked-Reads At 10x Genomics, we are committed to ...
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What is limiting the accuracy of genome sequencing today?

What are the current limiting factors of genome sequencing accuracy? By accuracy I mean a closeness relation between the sequenced genome and the finally assembled (I am not sure whether there is a ...
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Polymerase Cycle Assembly (PCA) is not working (Only primrs in EF Gel)

Helllo All 👋! I am working trying to assemble dsDNA fragments (for further golden gate domestication) via polymerase cycle assembly (PCA). After designing the required oligonucleotides with overlap ...
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Are there known genome sequencing issues in E. coli?

Despite the fact that the human genome project was declared "complete" in 2001, there are even now still gaps due to difficult-to-sequence regions of the genome such as telomeres and ...
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Genotyping technologies maintaining phase

My professor made the statement that genotyping technologies don't maintain phase. What exactly is meant by this phase? I guess I'm more confused on what's the difference between sequencing and ...
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What are primary reasons for the failure to localise/anchor sequences in genome assemblies?

My question concerns the incorporation of individual sequence reads into chromosomes during gene sequencing projects, especially those with larger genomes such as Drosophila melanogaster or Homo ...
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What is the difference between contig- and read-based sequence alignment?

I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused ...
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When to decide that two similar sequences are different genes or not?

Working on RNA-Seq data directed me to ask this question. In RNA-Seq jobs, after de novo assembly we have lots of transcripts with different rates of similarity (0 to almost 100 percent) that we ...
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How do we know which Eulerian path corresponds to the DNA sequence?

Bioinformatics textbooks explain one method to reconstruct the whole DNA sequence from multiple reads. The method builds a graph and finds a Eulerian path in it. The Eulerian path corresponds to a DNA ...
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What is known about the coding sequence of Factor H in the human genome?

Factor H is a protein coded in 20 domains. My question is whether these domains form some kind of repeat cluster in the human genome. Basically, I'm interested in the coding sequence from an ...
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Alignment of sequenced fragments in Next Generation sequencing (sequence assembly) [closed]

The NGS (Next Generation Sequencing) involves fragmenting the DNA to be sequenced. This is followed by attachment to beads or flow cells and then a localized PCR is conducted. Modified bases are added ...
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How the genome assembly be done after k-mer counting?

As far I know, before assembly of a genome, all k-mers from read should be counted. But after that, how the genome assembly be done? Is there any other thing needed along with k-mer counts? How the ...
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How is output of DNA assembler measured?

I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs. Many papers measure own algorithms and compare it against each other. There are basic metrics like: N50, N70....
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What is the difference between sequence alignment and sequence assembly?

I read the wikipedia page about sequence alignment and sequence assembly but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence ...
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What does the "cov" mean in a velvet assembler generated contig name?

A exmaple of a contig name generated by velvet assembler: NODE_127_length_39203_cov_244.873016 What does cov_244.873016 mean? ...
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How Scientists sequence, assemble and annotate plant genomes? [closed]

I previously read this question and this paper and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and ...
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Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
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Gibson assembly - primer design with A and T rich regions

I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: 5'...
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Assembly reconciliation

We have some bacterial genomes that were assembled using Spades, they were sequenced with and IonTorrent PGM. There are many assemblers and they give different results. I was interested in a tool ...
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Why is assembling paired end illumina without any input parameters an important problem?

In one of the comments in this question about multiple sequence alignment, it was stated @5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any paired ...
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Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?

I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this ...
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How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: how ...
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What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...
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