All Questions
Tagged with assembly genome-sequencing
6
questions
0
votes
1
answer
80
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
5
votes
1
answer
89
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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 ...
- 280
1
vote
1
answer
88
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 ...
- 359
2
votes
2
answers
335
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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
...
- 359
3
votes
2
answers
346
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Separation of mixed plasmid DNA sequences post whole-plasmid sequencing
Imagine a DNA sample containing a mixture of different intact plasmids. These samples are sequenced using either MiSeq or HiSeq sequencing. Would it possible to assemble these plasmids post-sequencing ...
- 155
3
votes
1
answer
171
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Can the canu assembler output a fastq file of the final assembly just like HGAP4?
I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
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