Comments (4)
moold
commented on June 14, 2024
Could you provide the config file and how about the genome size?
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yilunhuangyue
commented on June 14, 2024
the genome size is about 300M and the config siz is like this:
task = 1212
genome = genome.fa
sgs_fofn = sgs.fofn
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moold
commented on June 14, 2024
I guess you ran pilon with bwa, while ran NextPolish with minimap2, see FAQ vi. You can try to use option: sgs_options = -max_depth 100 -bwa. Our tests shown the accuracy of polished genomes using minimap2 will less than bwa in some situations.
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yilunhuangyue
commented on June 14, 2024
Yes, i run Nextpolish with minimap2. I will try use bwa and compared the result. Thank you~
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Related Issues (20)
- how to deal with "N" HOT 1
- Polish with raw or corrected ONT reads? HOT 1
- NextPolish slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT HOT 6
- Using Illumina Hi-C and Chicago data? HOT 4
- How to use Nextpolish on NextDenovo draft assembly HOT 2
- Need information related to example given in NextPolish Software under the folder test_data HOT 4
- MissAssembly Correction using NextPolish (Need Suggestions) HOT 1
- nextpolish2.py never stop HOT 6
- Adding Hisat2 instead of BWA HOT 1
- error of generate_lqseqs_from_cluster HOT 3
- repeat regions HOT 5
- Empty bin directory after installation? HOT 2
- User defined alignment pipeline for short- and long-reads HOT 2
- [question] combine with medaka or not? HOT 3
- run nextplolish2.py sleep HOT 8
- Ignore the secondary alignment HOT 2
- Test run failed at map_genome: "[gzclose] buffer error" HOT 3
- Installation failure with multiple definition of 'rle_auxtab' HOT 2
- db_split failed: HOT 3
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