What is the best de novo assembler for bacteria?

Question

[thustar]

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!

[Medhat]

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

[Brian Bushnell]

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.

Answer 1

[Steven Lakin]

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.