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Hello,
At step 14 following error message occured:
Error running command: perl /media/smrtanalysis/Linux_Data/SqueezeMeta/scripts/../bin/MaxBin/run_MaxBin.pl -thread 11 -contig /media/smrtanalysi…
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hello!
I read your guideline and followed it using my bam file.
But, I don't understand the difference among simple mode, somatic mode, amplicon mode.
Could you explain the difference briefly??…
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Hi, I was just wondering if there is a way to provide a larger file as opposed to a small amplicon that you normally could easily supply on the command line?
On a related note, do you know if the…
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We submitted 40 sequences that passed SIGNAL metrics, but 15 were rejected due to frameshifts. We should add this level of reporting/QC to ensure sequences are ready for GISAID.
> Your submission B…
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Add dockerfiles for all the tools needed by the [vector short read alignment pipeline version 1.1.1](https://github.com/malariagen/pipelines/blob/c7210d93628aaa31f26baa88a92e10322368b78e/docs/specs/sh…
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Add pipeline support for running https://github.com/jts/ncov-tools
Issue created at ncov-tools repo: https://github.com/jts/ncov-tools/issues/2
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Hi guys!
We will be sequencing several hundred virus strains, and I am looking for a pipeline to do de-novo assembly and variant calling.
Since I have been working with nfcore @drpatelh in the…
ktrns updated
4 years ago
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Hi Simon,
thanks for the update of the MetONTIIME script, it's great to get the feature_table now for every taxalevel!
I have another short question about the pipeline. Why is 1400 bp with a window…
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Hi Matt,
We're using the amazing ARTIC protocol for Covid-19 sequencing but observe that there is sometimes significant individual-amplicon dropout. The amplicons are relatively short (~400). Would…
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Dear All,
We have done V1-V9 illunima sequencing for our amplicon sequence analysis. Ive executed standard QIIME2 pipeline using GG database. But in qiime2 results, i didnt get any species level info…