Newbler 3 assembler download - assembly of highly heterozygous genome

Question

[joneill4x]

Hello all,

Does anyone know where I can obtain a copy of the Newbler v3.0 assembler?

I have managed to download and install v2.9, having obtained it from from the 454 official website. Link: http://454.com/contact-us/software-request.asp

However, v2.9 has a max read length of 2000, while v3.0 has a max read length of 30000. This is important for my work.

In the paper "The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history", the authors use Newbler v3.0 to assemble long reads (length < 29000). http://biorxiv.org/content/biorxiv/early/2016/07/18/064428.full.pdf

I am making a de-novo assembly of my own for a highly heterozygous diploid species and seek to emulate their assembly process.

Thank you, Joe

Thank you

Answer 1

[felipe.zoujiro]

Hi everyone,

This more than an answer to this issue is a request/question that hopes you can help me, guys!

The link you mentioned (http://454.com/contact-us/software-request.asp) is dead. I guess 454 is out-of-market. So, I am wondering if any of you that have obtained the Newbler software either v2.9 or v3.0 can share it with me?

Thanks in advance,

Felipe

Answer 2

[lexnederbragt]

Have you tried using http://454.com/contact-us/software-request.asp again? That should now give you version 3.0.

[joneill4x]

Hi lexnederbragt, thanks for your answer. I tried using that link again just now, but it still is showing only v2.9 available for download.

Answer 3

[salgado7]

Hi all, please look into this link C: Is Newbler still available for download