Questions tagged [assembly]
Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or transcripts assembly, in which case the original sequences are RNA transcripts.
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How does one distinguish nuclear DNA from mitochondrial DNA when doing WGS?
I'm interested in doing de-novo sequencing but also phylogenetic analysis. In particular, after de-novo sequencing and annotating the genome, I need to align the CO1 gene and the nuclear 28S rRNA gene ...
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MetaQuast for assembling samples from complex communities
I'm working with whole genome metagenomic samples from human skin, and I'm using MEGAHIT for assembly and MetaQuast for evaluation. However, MetaQuast requires a list of reference genomes for the ...
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DNA genome string reconstruction from k-mer
I have the following quiz question, but the Pattern1 for both (ACC|ATA) and (CGA|ACT) are unique (just grep for ...
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How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?
NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely)
For a Complete genome it's fairly ...
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Assemble Anaeroplasma species genome from metagenomic PacBio data
I have a fasta file containing reads generated by PacBio HiFi whole genome sequencing of a feces sample from mouse.
I would like to use this dataset to generate an assembled circularized genome for an ...
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How can I improve or otherwise investigate an unreliable genome tree?
Summary My genome tree doesn't agree with my gene trees and I get the feeling that my genome tree might be wrong, possibly due to long branch attraction, but I don't know how to check/fix it.
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Why must a maximal non-branching path be a contig?
The following is from Bioinformatics Algorithms:
Fortunately, we can derive contigs from the de Bruijn graph. A path in a graph is called non-branching if in(v) = out(v) = 1 for each intermediate ...
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How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?
I want to display E.coli BW25113 (GenBank: CP009273.1) strain in UCSC browser. This strain is not listed in http://microbes.ucsc.edu/ browser. How can I display E.coli BW25113 assembly in the browser?
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Extract sequence context of high-degree nodes in assembly graphs
I often use metaSPAdes to assemble short reads from human microbiomes. My simplified understanding of short-read de Bruijn graph assemblers is that they fail where ambiguous paths cannot be resolved. ...
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How to manually curate a genome assembly for sequence variation or error?
I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, ...
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How to improve a genome assembly using Dovetail and PacBio assembly?
I have more of a conceptual question. I have two genome assemblies from the same plant, one from Dovetail technology (~998 Gb) and another is PacBio HiFi assembly (~1.1 Gb). The Dovetail assembly is ...
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Length of Contigs in Transcriptome and Whole Genome Assembly
Why are there shorter contigs from transcriptome assembly than from a whole genome assembly? I know the difference between transcriptome and genome, but don't really understand what contigs are in the ...
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Comparing homozygosity of k-mer plots
Attached are two kmer plots from two closely related species. Is that safe to say that the one on the left has higher homozygosity than the one in the right k-mer plot, due to a low to almost flat ...
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Understand this Kmer plot from Merqury?
The attached figure is generated based on Illumina reads from multiple individuals compared to genome assembly. Looks like there are a lot of kmers are reads only (grey colored). Also, a blue peak (2x ...
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What are some ways to check metagenomic bin quality?
I am new to metagenomic binning. I've used CheckM in order to estimate completeness and contamination values, and most of my bins of interest appear to have good values. My workflow was pretty ...
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