Comments (4)
Thanks for trying DrPRG! @mbhall88 is unfortunately on holiday for a couple of weeks, and I think really only he can help. Sorry for the delay!
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Hello Iqbal,
Thank you for your quick reply. It's not a problem at all, we researchers need breaks once in a while after all 😃 As alternative we're also currently trying Clockwork for Mycobacterium tuberculosis, and I'm astounded to find out that the link in the official WHO document leads to your GitHub too. I'll let you know if we have succeded on using your program. Thanks for your hard work.
Cheers!
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Hi there! ok good. I just wanted to clarify one thing - DrPRG and clockwork do different things. Clockwork does decontamination of human reads, and SNP/indel calling, and optionally you can run Mykrobe also to predict resistance. But if you just want resistance prediction while waiting for Michael to return, you don't need the whole of clockwork, Mykrobe alone will do. You probably know this, but I just wanted to check
(Yes, i was amazed to find the WHO mentioning clockwork!)
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Hi @ptrmtb which container are you using? i.e. how are you pulling the container and what address? And what commands are you running to use index and what is the output?
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Related Issues (20)
- False positive argmatch results HOT 1
- Run drprg HOT 4
- Add grammar for specifying variant "expert" rules
- Benchmark figures HOT 7
- Parse pandora VCF to detect minor alleles HOT 46
- Update pandora and make_prg HOT 2
- Deal with gene absence HOT 9
- Add some common resistance-conferring mutations that do no exist in population graph HOT 8
- Notice partial gene deletion that spans start codon HOT 8
- Targeted sequencing mode HOT 1
- Disruptive in-frame indels HOT 3
- Lineage calling HOT 1
- Add install instructions to README.md
- How do i pronounce this tool name HOT 1
- Installation_error HOT 2
- Collate_drprg_results HOT 1
- Paired-end fastq files HOT 1
- Missing expected output file /test/outdir/discover/denovo_sequences.fa HOT 5
- Index is not valid, missing files error HOT 2
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