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lvrcek / GNNome-assembly

Learning to untangle genome assembly with graph neural networks.
MIT License
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Hifiasm_error correction_question #9

Closed yao-chenxin closed 2 years ago

yao-chenxin commented 2 years ago

Hi,author: I would like to ask you how the reads after Hifiasm error correction are obtained from the bin file? What software is used? The original sentence in the article: We first error-correct reads with hifiasm [16], thus reducing amount of mismatches, insertions, and deletions in the reads.

I am looking forward to your reply. Thanks.

lvrcek commented 2 years ago

Hi yao-chenxin,

We extract the error-corrected sequences from the FASTA file. Apart from the bin file, you should also see a file whose name is ending in .ec.fa. This is the file where the error-corrected sequences are stored.

For example, if you run Hifiasm with the following command:

./hifiasm -o output -t 32 --write-paf --write-ec  reads.fastq

You should see a file called output.ec.fa inside your working directory.

Let me know if you have any firther questions!

yao-chenxin commented 2 years ago

Hi,author: Thank you very much for your reply.

With best wishes!

At 2022-08-03 11:32:36, "Lovro Vrček" @.***> wrote:

Hi yao-chenxin,

We extract the error-corrected sequences from the FASTA file. Apart from the bin file, you should also see a file whose name is ending in .ec.fa. This is the file where the error-corrected sequences are stored.

For example, if you run Hifiasm with the following command:

./hifiasm -o output -t 32 --write-paf --write-ec reads.fastq

You should see a file called output.ec.fa inside your working directory.

Let me know if you have any firther questions!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>