How to remove chimera from 16S Sanger contigs · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

How to remove chimera from 16S Sanger contigs

Hi,

I have a bunch of 16S Sanger sequences, and I used UGENE to trim and edit sequences, then generated the contig using CAP3 embedded in UGENE. I submitted most of the sequences in the GenBank and received their accessions, but a few of them failed to be submitted and I received a uchime report for the chimeric sequences detected in these contigs. Could you please help me know how to use this report to clean the contigs from chimeric sequences?

Thanks!

sanger-sequencing chimera uchime

• 711 views • link

updated 2.9 years ago by Ram

• written 2.9 years ago by eimanpharmacist •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Unsure why HLA imputation job rejected from Michigan Imputation Server
written 4.4 years ago by 4galaxy77

I have submitted a chr6 .vcf file to impute HLA genotypes in the cohort of samples I have working with. I received this QC report: …
Which files from PacBio output files to use in downstream analysis in R
written 4.9 years ago by eimanpharmacist •

I just received Pacbio sequences of 16S gene from the core facility. After download, I got 5 files for each sample with following suffix: ``` …
UGENE Workflow Designer
written 5.9 years ago by AfinaM •

Hi everyone, I am currently trying to create my own pipeline using UGENE where we are able to create our own custom pipeline using its …
RNA de novo assembly - blasts - KEGG - GO
written 6.4 years ago by dimitrischat

Hello, I am a phd candidate to bioninformatics and with (almost) 0 guidance. Seeking help here.. I was asked to do a de novo RNA …
Running Genbank check prior to submission?
written 7.1 years ago by stacy734 •

Hi everyone, I recently submitted an insect genome to Genbank, and received back a very helpful report showing some contigs had contaminating bacteria. Most of …
why capt3 tool cannot efficiently find the overlapping contigs?
written 11.0 years ago by seta

<p>Hi all,</p> <p>I did transcriptome assembly on illumina PE, 100 bp reads at different k-mers, and now try to merge resulting assemblies. So, I pool …
generation of contigs from sanger sequencing
written 11.2 years ago by jasbadesha27 •

Hi, I have a lot of sanger sequences to assemble into the contigs. To be more precise, I used 50 samples for 3 primer pairs …
Inconsistent Cap3 Assembly
written 13.1 years ago by hbw

<p>This question is cross-posted at <a href='http://seqanswers.com/forums/showthread.php?t=31895'>SeqAnswers</a> with the alignments. I have 5 related EST sequences and I want to assemble contigs. I am using …
How To Manually Check Your Putative Chimeric Sequences
written 13.7 years ago by samlambrechts299

<p>Hi everybody,</p> <p>Various sources tell me it is not recommended to blindly discard all sequences flagged as chimeras by tools such as Chimera Slayer and …
Cap3 Integration Of Velvet And Newbler Assemblies
written 13.7 years ago by tommivat

<p>I am conducting de novo assembly of ~33Mb genome using 454 and Illumina reads. I cannot use MIRA, since I have ~80M Illumina reads (would …