Go Back   SEQanswers > Applications Forums > De novo discovery

Similar Threads
Thread Thread Starter Forum Replies Last Post
Retrieve read IDs from SPAdes contigs lasantos Bioinformatics 0 06-12-2019 11:14 PM
SPAdes contigs vpi Bioinformatics 3 12-02-2015 04:49 PM
SPAdes trusted contigs aimc Bioinformatics 0 01-12-2015 10:22 AM
Velvet misassembly with chromosome and plasmid hkg De novo discovery 4 01-08-2015 08:19 AM

Thread Tools
Old 08-09-2019, 08:58 AM   #1
Junior Member
Location: USA

Join Date: Apr 2019
Posts: 2
Default SPAdes duplicate contigs between chromosome and plasmid

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?

causland is offline   Reply With Quote

assembly, de novo, spades

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:56 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO