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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Comparing loci across catalogs

Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of a plant species, and have aligned my paired-end RAD reads to a reference genome (using GSNAP). The goal ...
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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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BUSCO results apparently inconsistent

I have two assemblies obtained from two different softwares for the same run data. In one of them, I get a BUSCO score of 69,4%. In the other one, I get 68,5%. The first assembly covers a 99,7% ...
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How to de novo hybrid assemble with Pacbio CCS and Illumina PE reads

I would like to perform de novo genome assembly on a diploid microalgal strain. I have two datasets: PacBio CCS/HiFi reads, low coverage. Illumina PE 2x150 (standard shotgun) Does anybody have any ...
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Mapping contigs back to samples from co-assembled metagenome

In an attempt to increase the quality of our metagenomic assembly and ensure we capture low abundance species we are co assembling ~20 samples. However after the assembly we need to perform some ...
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Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)

Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment. Is there a way for me to do a "...
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How do you set the coverage in PacBio's Sequel II?

I am reading the Whole Genome Sequencing for de novo Assembly Best Practices Use the Sequel II or IIe System and SMRT® Cell 8M to sequence to desired coverage depth for complexity of genome 10- to 15-...
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Can someone help me estimating the runtime of the pipeline applied by the vertebrate genome project?

The vertebrate genome project (VGP) has a lot of interesting publications such as this one. The rough pipeline is outlined below: Here the pipeline in more detail: While the paper describes all the ...
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How to know if the DNA sequence has been assembled and why is it important to know how it was assembled?

I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences ...
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How to quantifiy of specific genes from shotgun metagenome?

I have googled a "lot", couldn't find any specific answer to the question. So, I am here seeking for your guidance. My question is similar to this. I have several metagenome (n=30). But for ...
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Trinity assembly from many samples

When you combine samples for de-novo transcriptome assembly with Trinity, do you suggest limiting the number of reads for each sample? I had read one of Matthew MacManes' papers awhile back suggesting ...
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Genome annotation

I have helped a lab sequence a mitochondrial genome. I used then MITOS to annotate the genome (warning them that I did it just for curiosity as I am not experienced). They submitted the sequence and ...
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where to find sample contig data

Where or How can I find contigs? I am trying to learn Bioinformatics and I want to make a reference-based gene search. I also want to align contigs with a given reference sequence. From NCBI other ...
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Denovo, Stacks: Getting an “ambiguous redirect” error

I tried running the following command ...
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Genome QC + Assembly Pipeline semantics

I’m trying to create a pipeline for genome assembly. How best can I “redirect/pipe” from existing fasta files (or files in general) to other steps of the pipeline? I was thinking of going from the SRA ...
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Quast duplication ratio and mismatches percent

When analyzing Quast results it seems that it doesn't calculate mismatches and indels in a useful way if the "Duplication ratio" is over 1. For example, that's what I get for an assembly ...
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Gold standard benchmark

This page is claimed to contain a gold standard benchmark for viral genome assembly. https://github.com/cbg-ethz/5-virus-mix The claim is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/ ...
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How to filter a genome assembly consistsing of a large number of contigs?

I did some de novo genome assemblies with Illumina PE data using SPAdes, whereas most of them consisting of a large number of contigs(>1000). I have several questions below. Do we need to filter ...
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Which one is a more convenient assembly?

I have developed a software for de novo genome assembly. Its performance varies gradually according to how much data you employ. At initial stages it often produces contigs that look like that when ...
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Repeat analysis on eukaryotic assemblies

I have a hundred insect genomes and I'm looking for repeated regions along these assemblies. First of all, I thought of using <...
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Is it possible to filter contaminated reads for raw PacBio sequences (not HiFi reads) before assembly?

De novo genome assembly for non-model organisms face the issue of bacterial contamination. For assembled contigs with mostly bacterial-like sequences (based on BLAST search), the entire contig can be ...
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Is there a simple command for outputting a tab delimited columns?

I am working on a fasta file and am writing my command in nano within command-line and executing using python, also within a command line. My objective is to get my command to provide me with a tab ...
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creating a tab delimited file

I am working on a project using a fasta file. I am writing my command in nano within command-line and executing using python, also within my command-line. I would like my command to provide me with a ...
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Is it possible to convert BAM file from one genome assembly to the other?

I Have multiple BAM files that are referenced to UCSC genome assembly GRCh37/hg19 that are read in different time frames. Now, I am planning a different studies that require assembling all the data ...
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Contamination on genome assembly

I had a question for the community. I have a genome of a new species that has been sequenced via 150pb Illumina paired-end. To verify the quality of the assembly I used the ...
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How to find all WGS assemblies accessions of a species

Some background Similar to the OP of https://www.biostars.org/p/377840/, I would like to programmatically BLAST a sequence to a local database of all WGS assemblies. Since this isn't feasible for the ...
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Interpreting contig alignments to a reference genome

I have applied two de novo genome assembly tools to data from the run SRR12707453, corresponding to a phage (I downloaded the data and have no relation with the authors of the study). Using rnaSPAdes ...
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Difference between paired-end, mate-pair and long read

I writing here because I have some questions for you. I wondered what the essential differences were between paired-end, ...
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PacBio long-reads impact in transcriptome de novo assembly?

We are strongly interested in assembly a good transcriptome of reference for a non-model organism and build a local database. We have sequenced the same individual with Illumina (150 millions of pair-...
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Genome assembly of SRR12196449 with SPAdes

I am trying to assemble the run SRR12196449 with SPAdes. The description of their project is: This project expected to standardize a method for amplification and ...
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How can I get or create a reference genome for Bacteria?

I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant ...
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RCSB API: limited returned result

Is there a limit of query results on RCSB API? Interestingly, no matter how to adjust my query criteria, only 10 assemblies are returned. Here is an example query json: (truncated from a longer query ...
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Resources to learn genome assembly workflow for small genomes (like viruses)

I have sequencing data of a few samples of a DNA virus. I'd like to learn de novo assembly of 'short read' data, to construct a scaffold and then count the abundance of each strain in the data. I ...
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Gap-fill assembly with PacBio reads

I would like to gap-fill (or correct) a mammalian-sized assembly for which we have BACs that have been sequenced with PacBio CLR data. I have seen there are pbm22/gcpp tools available for correcting ...
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Difference between genome assembly and genome sequence alignment to a reference to find structural variants

I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations. I've been ...
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How to fragment genomes into non-overlapping sequences of differing sizes?

I have bacterial chromosomes/plasmids that I have downloaded off refseq in a multi-fasta that I would like to fragment into non-overlapping fragments of between 1 kb and 15 kb. I have tried googling ...
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Bacterial DNA at the tail of transcriptome reads. What does that mean?

I am assembling a transcriptome obtained from the Internet. The transcriptome was extracted from a human cancer tissue that had been previously grafted into a mouse. I have detected that many ...
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Comparing gene abundances between metagenomes

My workflow until now: Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest Right now I have a ...
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Can SBOL encode DNA Assembly linkers?

Where in an SBOL file could you specify the linkers that would be placed as prefixes / suffixes between parts for assembly? Lets say you have a final construct of your design and want to assemble the ...
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Decontaminating RNA seqs for de novo transcriptome assembly and annotation of novel eukaryotes

I have raw paired-end RNA-seq reads for two novel eukaryotic species. Some background: the reads represent a copepod (arthropod) species each. The mRNA for each read set was obtained by extracting ...
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Gffcompare issue: 0 reference transcripts loaded

I am trying to use gffcompare to compare my assembled transcriptome to a reference gtf that contains information about small open reading frames (sORFs). The reference gtf was obtained by processing ...
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"megahit: command not found" after correct installation with miniconda

I want to use MEGAHIT (git: https://github.com/voutcn/megahit) to assemble metagenome shotgun sequencing reads (illumina). I install the package with the command <...
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