Question: What is the best de novo assembler for bacteria?
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gravatar for thustar
4.0 years ago by
thustar100
thustar100 wrote:

Hello, biostars!

I am working on a project on metagenomics. The first step is to assemble 100 bp reads into contigs of several thousand length. Therefore, I need a de novo assembler software to do this job. I do not and actually can not get the whole genome because the length of read is too small compared to the total length of a genome.

What de novo assember will you recommend?

Thanks!

assembly software • 1.4k views
ADD COMMENTlink modified 4.0 years ago by Steven Lakin1.5k • written 4.0 years ago by thustar100
1

after answering @Brain question, Generally speaking the best assembler depends on what you have This will help you to decide
Completing bacterial genome assemblies: strategy and performance comparisons

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

Best software to assemble bacterial genomes

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Medhat8.7k
1) How much data do you have?
2) From what sequencing platform?
3) What kind of metagenomic community/environment are you studying?
4) What kind of compute resources do you have access to?  Mainly, how much memory/how many cores on a single node.
ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Brian Bushnell17k
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gravatar for Steven Lakin
4.0 years ago by
Steven Lakin1.5k
Fort Collins, CO, USA
Steven Lakin1.5k wrote:

Brian's questions are important to answering this question, however, you may also find some success using a combination of Amos and CISA: Amos will output a series of files from various assembly methods, and CISA will integrate them into a combined, master contig file.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Steven Lakin1.5k
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