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## Shorah Version:
1.99.2
## Command to reproduce:
```
$ shorah amplicon -b my_sorted_bam.bam -f amplicon.fasta -d
```
> I have trimmed my read length to equal length prior to this step.
#…
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Develop a workflow that better supports the creation of additional amplicon target descriptions. At a minimum format unassigned for blast searching or integrate searching against a reference genome.
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Hi,
sorry, this is more of a question (or a feature request, we'll see).
We are processing amplicon data, from which we want to trim PCR primers. The amplicon is shorter than the invidual paire…
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Could I please clarify one technical question. It is stated in the article (https://academic.oup.com/nar/article/50/D1/D777/6426060#authorNotesSectionTitle) that mapping to the GreenGenes database was…
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I have a problem with VarDict 1.8.2 calling amplicon based sequenced samples. I attach a sample with a SNP and an indel that are not being called in this version or VarDict 1.6.0. Nevertheless, the SN…
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Hi! Thanks for the effort on this tool, definitely want it to work for us. We are utilizing the QIAseq primer extension design, meaning there is only a single primer region we are concerned about. …
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Raising this issue to be followed up once we have a release candidate to evaluate.
Theo Sanderson spotted that if we look at spike 142, and colour a tree by genotype at that position, it looks a b…
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Hi mate!,
Love your program it has become my default to go for clustering and consensus.
I have been using it with the error below sporadically poping sometimes, but recently it is happening e…
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**Describe the bug**
When trying to simulate reads with length greater than 400, I get an IndexError: list index out of range error
**To Reproduce**
Steps to reproduce the behavior:
` python gen…
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Dear authors,
Thank you for your work, I was testing your software on several datasets and I obtained this error message:
```
[raven::] loaded 9004 sequences 0.110631s
[raven::Graph::Construct] …