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.

Filter by
Sorted by
Tagged with
0 votes
1 answer
14 views

How is an X chromosome encoded into a fasta string?

A human "X" chromosome has a centromere and two "identical" chromatids. If the chromatids are not identical, this fact is not assembled, correct? The fasta string for a chromomsome ...
4 votes
1 answer
25 views

How to promote assemblies into genomes in NCBI?

Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed. I'm working with Drosophila subobscura. (spring fruit fly) I see here https://www.ncbi.nlm.nih.gov/data-...
1 vote
3 answers
62 views

How can I assemble my genome from raw files?

I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF). How can I assemble it? And does assembly provide any further ...
2 votes
1 answer
20 views

need bam file for pilon

I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file. How do I make a BAM file of the resulting assembled.fasta?
  • 133
2 votes
1 answer
46 views

What is the best way to process yeast genomes?

I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis. I have a reference genome (S288C) to use for ...
  • 133
3 votes
1 answer
41 views

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 ...
  • 257
1 vote
1 answer
14 views

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 ...
  • 13
1 vote
1 answer
89 views

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 ...
  • 143
2 votes
1 answer
26 views

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 ...
  • 627
0 votes
2 answers
30 views

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 ...
  • 1
2 votes
2 answers
36 views

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. ...
  • 627
0 votes
0 answers
11 views

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 ...
0 votes
1 answer
55 views

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 ...
  • 127
5 votes
1 answer
25 views

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?
  • 371
10 votes
2 answers
150 views

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. ...
  • 483
0 votes
0 answers
42 views

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, ...
0 votes
1 answer
49 views

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 ...
0 votes
1 answer
48 views

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 ...
  • 13
1 vote
1 answer
66 views

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 ...
0 votes
1 answer
107 views

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 ...
0 votes
2 answers
53 views

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 ...
  • 627
0 votes
1 answer
46 views

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% ...
0 votes
1 answer
198 views

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 ...
0 votes
0 answers
12 views

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 ...
  • 143
1 vote
1 answer
46 views

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 "...
  • 1,498
0 votes
2 answers
56 views

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-...
  • 270
5 votes
1 answer
77 views

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 ...
  • 270
0 votes
2 answers
92 views

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 ...
1 vote
1 answer
59 views

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 ...
1 vote
1 answer
198 views

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 ...
  • 151
0 votes
2 answers
87 views

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 ...
1 vote
1 answer
126 views

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 ...
  • 73
-1 votes
2 answers
107 views

Denovo, Stacks: Getting an “ambiguous redirect” error

I tried running the following command ...
  • 19
0 votes
3 answers
57 views

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 ...
1 vote
1 answer
60 views

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 ...
3 votes
2 answers
77 views

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/ ...
0 votes
0 answers
120 views

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 ...
  • 81
1 vote
1 answer
73 views

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 ...
1 vote
0 answers
15 views

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 <...
  • 123
1 vote
2 answers
322 views

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 ...
1 vote
1 answer
56 views

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 ...
0 votes
2 answers
438 views

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 ...
0 votes
1 answer
91 views

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 ...
3 votes
2 answers
143 views

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 ...
3 votes
1 answer
110 views

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 ...
1 vote
1 answer
95 views

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 ...
1 vote
1 answer
512 views

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, ...
2 votes
1 answer
116 views

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-...
2 votes
2 answers
250 views

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 ...
1 vote
2 answers
117 views

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 ...
  • 13