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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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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