Questions tagged [scaffold]

A set of contigs, the order of which corresponds to consecutive genomic locations. Contigs can be scaffolded using a reference genome or optical mapping.

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Longstitch error make: command: Command not found *** No rule to make target

I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error. <...
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Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?

I'm currently doing my thesis with the topic of phylogenetic analysis and is taking references from the previous person in my university (who have done the same topics but different species). They ...
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RagTag patch error--"Tuple index out of range"

This question was also asked on GitHub I'm trying to correct a long-read assembly with a short-read scaffold; I'm hoping to fill in the short gaps in the scaffold with the matching long-read sections. ...
schmiggle's user avatar
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Phylogenetic tree building from proGenomes database for shotgun metagenomics

For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance. I’m ...
MagíBC's user avatar
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Phylogenetic tree rooting in shotgun metagenomics

But I have some weeks fighting with this issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account tree distance branches ...
MagíBC's user avatar
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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 ...
juanjo75es's user avatar
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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 ...
Reza Rezaei's user avatar
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Is there any value in scaffolding the output contigs of MEGAHIT assembler given a metagenomic dataset?

As far as I understood, for most assembly programs, the scaffolding step takes into consideration paired-end information in order to get from contigs (contiguous sequences) to scaffolds (longer ...
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Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while ...
Leah's user avatar
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Genome scaffolding

I have assembled a virus genome using Ray resulting in approximately 5000 contigs. Now I want to build a scaffold of those contigs to get the full genome (I am aware of the fact that there might be ...
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Can I run STAR without an annotation file?

I wish to use Rascaf to scaffold a fragmented draft genome. For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome. So, I indexed the draft genome with STAR like this: <...
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Scaffolding a genome with hybrid data

I am assembling a ~500MB genome, and have ~150x long reads and ~200x 150bp PE short reads, with a ~400bp insert size. I've done a lot of work with minimap+miniasm, and have what I think is a good set ...
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Installing Sibelia for Ragout on Mac OSX

I am trying to use Ragout: https://github.com/fenderglass/Ragout to fill the gaps in my de novo genome assembly. You can access the article freely here: https://www.ncbi.nlm.nih.gov/pubmed/24931998 ...
Biomagician's user avatar
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How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?

Low coverage MinION reads should be useful to close gaps and resolve repeats left by short-read assemblers. However, I haven't had any success with the software I know about. I'm aware of the ...
Tom Harrop's user avatar
4 votes
2 answers
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Reordering scaffolds according to a reference without a genetic map

I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
l0o0's user avatar
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What causes the difference in total length of assembled contigs and scaffolds in SOAPdenovo2?

I use SOAPdenovo2 to assemble a large genome (4.8G) using ~20X paired-end reads. The total length of contig sizes is 6.3G while total length of scaffolds is 2.7G. Note that this is a haploid genome, ...
user8095614's user avatar