Hi all,
Has anyone had any issues with SPAdes outputting duplicate sequences between plasmid and chromosome assembly outputs? I have an assembly ready to submit to NCBI but they won't take it because of 74 instances of a contig being found in a plasmid that is also found in the chromosome.
I am going to be parsimonious in my assumption that this is a result of assembly and not perhaps recombination between the chromosome and the plasmid. I tried blasting the sequences that were marked as having a duplicate to see if they are more likely in other genomes of the same species to align to chromosome or plasmid sequence, but in many instances they could go either way (no overwhelming alignment to either chromosome or plasmid sequences in GenBank).
Has anyone else run into this issue before, specifically with SPAdes?
Thanks
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
Latest Articles
Collapse
-
by seqadmin
The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...-
Channel: Articles
11-06-2024, 07:24 PM -
-
by seqadmin
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
Channel: Articles
10-18-2024, 07:11 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 11-08-2024, 11:09 AM
|
0 responses
198 views
0 likes
|
Last Post
by seqadmin
11-08-2024, 11:09 AM
|
||
Started by seqadmin, 11-08-2024, 06:13 AM
|
0 responses
145 views
0 likes
|
Last Post
by seqadmin
11-08-2024, 06:13 AM
|
||
Started by seqadmin, 11-01-2024, 06:09 AM
|
0 responses
80 views
0 likes
|
Last Post
by seqadmin
11-01-2024, 06:09 AM
|
||
New Model Aims to Explain Polygenic Diseases by Connecting Genomic Mutations and Regulatory Networks
by seqadmin
Started by seqadmin, 10-30-2024, 05:31 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
10-30-2024, 05:31 AM
|