genome assemlers specifications

Question

[midox]

Hello,

I am new in the field of assembly I wanted to know which element among these assemblers working on long reads (> 1000BP) or short reads (<1000pb).

• Abyss
• Cabog
• Newbler
• Mira
• MaSuRCA
• SGA
• SoapDenovo2
• SPAdes
• Velvet

Thank you for your reply friends

Answer 1

[Bert Overduin]

To answer questions like this Google is always your best friend.

A simple search for "comparison of genome assemblers" gives me, amongst others, the following PLOS ONE papers:

Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

Answer 2

[st.ph.n]

It also depends on which sequencing platform you got your data from. Some of those are specific to Illumina, while others are 454 specific. It also depends on whether or not you're doing de novo assemblies or reference based assemblies. And of course, what your end goal is, and what you expect to find. As Bert stated, Google is your best friend.