SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how do i reduce misassemblies in spades? evolino Bioinformatics 0 10-30-2017 09:22 PM
SPAdes 3.9.0 on MacOS Sierra (10.12.1) osilander Bioinformatics 3 11-04-2016 10:39 AM
Complexity Time SPADES assembler mido1951 Bioinformatics 2 01-30-2016 05:12 AM
SPAdes contigs vpi Bioinformatics 3 12-02-2015 04:49 PM
SPAdes: with different read length bio_informatics Illumina/Solexa 6 06-10-2015 09:04 AM

Reply
 
Thread Tools
Old 02-08-2020, 05:45 PM   #1
bioramg
Junior Member
 
Location: South Korea

Join Date: Apr 2014
Posts: 3
Default SPAdes assembler

Hello,
I tried to assemble a mitochondrial genome assembly with SPAdes assembler using pair-end Illumina and Nanopore sequencing data. The size of the Illumina data is 18 GB and when I do hybrid assembly after trimming adapters, it showing that Memory is insufficient to run this program and requires at least 389 GB RAM. But, I am having 188 GB RAM.
Then, I used BBmerge commands to sort out this issue. But when I run pair-end reads using bbmerge-auto.sh command, its saying that "try increasing the -Xmx flag and using tool specific memory related parameters".

Please suggest me how to do hybrid assembly with both Illumina and Nanopore data?
bioramg is offline   Reply With Quote
Old 02-09-2020, 08:28 PM   #2
SNPsaurus
Registered Vendor
 
Location: Eugene, OR

Join Date: May 2013
Posts: 516
Default

Is your 18 Gb of Illumina data pure mtDNA or mtDNA plus nuclear? If it is pure mtDNA then you probably have many thousand-fold coverage of the mitochondrial genome and you can reduce the number of reads used as input (bbtools reformat will do that if you give the paired-end reads as in= and in2= and then use reads=10000000 or some other number). If it is not pure mtDNA then you probably still have high coverage and could cut the input by 3/4s.
__________________
Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com
SNPsaurus is online now   Reply With Quote
Reply

Tags
bioinformactics, bioinformatic analysis, bioinformatic tools, ngs analysis platform

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 11:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO