Need information related to example given in NextPolish Software under the folder test_data

[DrNavi]

Hi all,

I am trying to use NextPolish tool to polish my draft assembly. First I wanted to understand about the example data provided in the tool under the folder test_data. The folder contain these files: ~/NextPolish/test_data/hifi.fasta.gz ~/NextPolish/test_data/hifi.fofn ~/NextPolish/NextPolish/test_data/hifi.run.cfg ~/NextPolish/NextPolish/test_data/lgs.fofn ~/NextPolish/NextPolish/test_data/lreads.fasta.gz ~/NextPolish/NextPolish/test_data/raw.genome.fasta ~/NextPolish/NextPolish/test_data/run.cfg ~/NextPolish/NextPolish/test_data/sgs.fofn ~/NextPolish/NextPolish/test_data/sreads.R1.fastq.gz ~/NextPolish/NextPolish/test_data/sreads.R2.fastq.gz

Here, In this file list, I am confused what is raw.genome.fasta file, Is this is the reference genome of the target specie from any database like NCBI, Ensemble etc ? this raw.genome.fasta file is used in run.cfg. Here is the run.cfg file content....

[General] job_type = local job_prefix = nextPolish task = default rewrite = yes deltmp = yes rerun = 3 parallel_jobs = 2 multithread_jobs = 3 genome = ./raw.genome.fasta genome_size = auto workdir = ./01_rundir polish_options = -p {multithread_jobs}

[sgs_option] sgs_fofn = ./sgs.fofn sgs_options = -max_depth 100

[lgs_option] lgs_fofn = ./lgs.fofn lgs_options = -min_read_len 5k -max_depth 100 lgs_minimap2_options = -x map-ont

Please, help me to understand this......

Another question is if I have only long read then do we only need to avoid/eliminate the sgs_option commands???

Looking forward to hearing from you

Regards, Dr. Naveed

[moold]

raw.genome.fasta is the assembly file to be polished. for Another question is if I have only long read then do we only need to avoid/eliminate the sgs_option commands??? Yes.

[moold]

see https://nextpolish.readthedocs.io/en/latest/OPTION.html

[DrNavi]

Dear Hu Jiang,

Thank you so much for clearing my confusions. I just have one more question. The sequencing company provide me only one nanopore fasta file named "KI.fasta.tar.gz". I did not get two long read file as mentioned in the example data. So in .fofn file I can only mention one read file. is that OK? Please, clear my confusion Thanks Regards, Dr. Naveed

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On Wednesday, February 15, 2023 at 06:09:47 PM GMT+9, Hu Jiang ***@***.***> wrote:  

raw.genome.fasta is the assembly file to be polished. for Another question is if I have only long read then do we only need to avoid/eliminate the sgs_option commands??? Yes.

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[moold]

Yes, but you need to decompress KI.fasta.tar.gz first.