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How to use Nextpolish on NextDenovo draft assembly #105

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DrNavi opened this issue Feb 15, 2023 · 2 comments
Closed

How to use Nextpolish on NextDenovo draft assembly #105

DrNavi opened this issue Feb 15, 2023 · 2 comments

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@DrNavi
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DrNavi commented Feb 15, 2023

Hi, I am Dr. Naveed, i am new to perform Genome Assembly. I have nanopore long read data and I successfully used NextDenovo to draft a fungus assembly. I have got nd.asm.fasta file after assembly from NextDenovo, 11 contigs are generated. Now, I wanted to polish my draft assembly using NextPolish tool. What command I can use for polishing because when I saw the tutorial, I found this command is used to make input file for long read polishing,

ls reads1.fq reads2.fa.gz > lgs.fofn

However, I just got one output file from NextDenovo, which I want to polish.....

I hope I made my question clear here..... I need guidance
@moold
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moold commented Feb 15, 2023

reads1.fq reads2.fa.gz are the nanopore long read data files, same input as NextDenovo

@DrNavi
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DrNavi commented Feb 15, 2023

Dear Moold,

I only get only sequencing file from the company, "KI.fasta.tar.gz

@moold moold closed this as completed Feb 16, 2023
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@moold @DrNavi