search

anganachakraborty / S-conLSH-2.0

Spaced-context based Locality Sensitive hashing for Alignment-free mapping of Noisy Long Reads. This is an upgrade of S-conLSH which can handle multiple simultaneous threads to achieve a better run-time performance.
GNU General Public License v3.0
1 stars 0 forks source link

Use in Metabarcoding? #1

Open SamMcGreig opened 3 years ago

SamMcGreig commented 3 years ago

Hello,

Firstly, thanks for an interesting paper to read this morning!

I usually work with Nanopore data in a metabarcoding context, and was wondering if you have any idea how effective S-conLSH would be for mapping amplicons (length of about 650 bases) to a database of barcodes.

Thanks, Sam

anganachakraborty commented 3 years ago

Dear Sam,

It's nice to hear that you are interested in S-conLSH. Ideally, S-conLSH can work for any alignment-free alignment. However, I haven't tested it for mapping amplicons. The length should not be a problem. Please give it a try and let me know.

On Mon, 15 Feb 2021, 7:54 pm SamMcGreig, notifications@github.com wrote:

Hello,

Firstly, thanks for an interesting paper to read this morning!

I usually work with Nanopore data in a metabarcoding context, and was wondering if you have any idea how effective S-conLSH would be for mapping amplicons (length of about 650 bases) to a database of barcodes.

Thanks, Sam

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/anganachakraborty/S-conLSH-2.0/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN7DP2ARG3BW6ONULU5JJF3S7EVARANCNFSM4XUYZ5EQ .

anganachakraborty commented 3 years ago

Dear Sam,

It's nice to hear that you are interested in S-conLSH. Ideally, S-conLSH can work for any alignment-free mapping. However, I haven't tested it for mapping amplicons. The length should not be a problem. Please give it a try and let me know.

On Fri, 19 Feb 2021, 11:36 pm Dr. Angana Chakraborty, angana89@gmail.com wrote:

Dear Sam,

It's nice to hear that you are interested in S-conLSH. Ideally, S-conLSH can work for any alignment-free alignment. However, I haven't tested it for mapping amplicons. The length should not be a problem. Please give it a try and let me know.

On Mon, 15 Feb 2021, 7:54 pm SamMcGreig, notifications@github.com wrote:

Hello,

Firstly, thanks for an interesting paper to read this morning!

I usually work with Nanopore data in a metabarcoding context, and was wondering if you have any idea how effective S-conLSH would be for mapping amplicons (length of about 650 bases) to a database of barcodes.

Thanks, Sam

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/anganachakraborty/S-conLSH-2.0/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN7DP2ARG3BW6ONULU5JJF3S7EVARANCNFSM4XUYZ5EQ .