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.

Filter by
Sorted by
Tagged with
1 vote
1 answer
20 views

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 ...
3 votes
1 answer
32 views

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 ...
0 votes
1 answer
93 views

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 ...
0 votes
0 answers
28 views

How to extract homologous sequence data from multiple .vcf.gz files?

I have short read data from multiple samples stored as scaffolds.vcf.gz files. I have some gene sequence of interest. I want to find the closest homologous sequence ...
3 votes
2 answers
367 views

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 ...
1 vote
1 answer
72 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 ...
2 votes
3 answers
219 views

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 ...
1 vote
0 answers
35 views

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 ...
4 votes
1 answer
2k views

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: <...
3 votes
1 answer
124 views

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 ...
3 votes
1 answer
107 views

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 ...
8 votes
1 answer
915 views

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 ...
4 votes
2 answers
342 views

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 ...
5 votes
1 answer
274 views

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, ...