Comments (1)
moold
commented on June 23, 2024
Hi, I'm sorry for this question bothers you or anyone else with a similar concerns, but it's a long story and I work for a commercial company, so I don't want to say too much about it.
However,
If you (or others) want the source code for nextPolish, I'd be happy to email it to you, after receiving your request email sent via a educational mail.
You can delete samtools or third-party software in the nextPolish directory, and then follow here to use your own alignment pipeline, and then only use NextPolish to polish the genome. The precision of the polished genome is the same as the default.
I'm not familiar with open source licenses, I randomly chose the GPL license after someone asked me to release the license, so if you have a better option, I can replace and update it.
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Related Issues (20)
- Reduction in genome size after polishing HOT 3
- 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
- Why there is no stats about changes when polished with nextpolish1.py or nextpolish2.py HOT 1
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