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What is the best de novo assembler for bacteria?

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
• 2,955 views • link
updated by Steven Lakin Steven Lakin • written by thustar • thustar 
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.
• 1 views • link
written by Brian Bushnell Brian Bushnell

1 answer

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.

• 1 views • link
written by Steven Lakin Steven Lakin

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