All Questions
7
questions
3
votes
2
answers
89
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/
...
- 359
2
votes
2
answers
335
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
...
- 359
0
votes
1
answer
137
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 ...
- 169
2
votes
1
answer
260
views
What is the meaning of these misaligned reads in a sequencing run?
I am analyzing some SARS-CoV-2 sequencing runs abd often find read alignments like the one in the image.
...
- 359
3
votes
1
answer
105
views
Viral genome finishing
I have assembled poxvirus genome using Ray. The assembly is good. Out of several thousand contigs I got, I was able to get one scaffold using Contiguator tool, which is about 90% of my genome. I have ...
- 719
4
votes
1
answer
96
views
Viral genome assembly using broad viral ngs pipeline?
I am trying to assemble RNA virus genome using Broad Viral NGS pipeline BROAD VIRAL NGS PIPELINE. I am two questions :
1) As this pipeline requires unaligned bam format as input, how do I convert ...
- 719
5
votes
1
answer
158
views
Viral Metagenomics
I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray (reference below) for de novo viral genome assembly before but I haven't done metagenomics analysis before.
...
- 719