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baoe / AlignGraph

Algorithm for secondary de novo genome assembly guided by closely related references
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Single Read Libraries #8

Open LeeBergstrand opened 9 years ago

LeeBergstrand commented 9 years ago

Hello,

I am very interested in utilizing your software for a project. However, we are using Ion Torrent PGM for sequencing and thus we only have a single read library, reference genome and Denovo contigs.

Is have paired reads necessary for your implementation?

baoe commented 9 years ago

Hi,

Thank you for your interest in AlignGraph. I'm afraid the current version of AlignGraph can only support Illumina reads.

We are currently working on accommodating long reads, but this may take quite a lot of time.

Best, Bao

LeeBergstrand commented 9 years ago

Hello, again.

Do you know of any other software analygous to your own that can deal with long reads?

Cheers, Lee

baoe commented 9 years ago

Hi, Lee,

I haven't seen any paper for long reads but this one is for Sanger reads: Gnerre,S. et al. (2009) Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biol., 10, R88.

Best, Bao

From: Lee Bergstrand [notifications@github.com] Sent: Sunday, May 10, 2015 7:31 AM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] Single Read Libraries (#8)

Hello, again.

Do you know of any other software analygous to your own that can deal with long reads?

Cheers, Lee

— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/8#issuecomment-100647261.