Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Low K-mer coverage from a SPAdes assembly berthenet De novo discovery 2 02-05-2018 12:59 AM
Assembly vs. SNPs fishinvest Bioinformatics 3 04-03-2013 11:50 AM
Could there be no SNPs in a homozygous genome assembly? Lisa0508 General 7 08-20-2012 07:31 PM
newbler assembly ... padding and SNPs jnfass De novo discovery 12 06-09-2011 04:58 AM
how to validate SNPs and Indels after assembly? sulicon Bioinformatics 9 02-25-2011 05:27 AM

Thread Tools
Old 03-19-2018, 07:21 AM   #1
Location: Mainz, Germany

Join Date: Mar 2017
Posts: 21
Default SNPs detected in spades Assembly


we assembled one 150bp paired-end illumina sample with spades 3.10 and got about 400 contigs with a size of > 1kb.

Afterwards we scanned for SNPs with samtools/varscan with the same fastq-files in the assembly made out of these.
I know this doesn't make much sense :-), but samtools called some SNPs and we can see them in IGV, so they are really there.

How is this even possible, that we find a SNP with the same fastq files, of which the assembly is made of?

Last edited by iltisanni; 03-20-2018 at 05:02 AM.
iltisanni is offline   Reply With Quote

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 05:52 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO