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### Setup
Using:
```
3.8.1 (default, Jan 8 2020, 16:15:59)
[Clang 4.0.1 (tags/RELEASE_401/final)]
CPython
macOS-10.15.3-x86_64-i386-64bit
1.76
```
If you run:
```
from Bio.Sequencin…
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Hello,
I am trying to use snippy 4.6.0 via miniconda3 on Linux and the output given indicates my samples have 0 variants compared to the reference genome.
The created snps.csv has no data in it and…
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I think. clears up if ( removed from path. testing further once I reinstance with more ram (millstone really doesn't like it when it runs out of memory and gets very quickly into an unusable state -i…
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**Problem**
I currently have several snakemake workflows that require different environments on a per-rule basis when running within a docker container. I want the creation of the docker container to…
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Hello developers,
Thank you for developing a nice benchmarking tool. How to generate reference genomes in json format for BinBencher assessment? I couldn't understand from the documentation…
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Hi,
Thank you for developing the wonderful TEPID tool.
I have learned that the tepid-discover using concordant, disconcordant and split-reads bam as inputs. I was wondering if it is possible tha…
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Does anyone (e.g., @ilveroluca or @avilella) have any thoughts on the performance of `bwa mem` when run with a shared memory index (`bwa shm`)? I've found there to be a 24% performance penalty when u…
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Hi,
I used bwa mem to compare hic data to p-utg files and did some filtering on the results. It was found that there were very few hic signals on some short unitigs. I would like to ask whether hifia…
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Setting read groups (when “automatically assign ID” is selected) does **not** assign `SM` tag, which is a requirement. This causes downstream issues with Picard etc.
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I ran Picard's ValidateSamFile on my aligned human exome sequencing data, and encountered the following:
```
ERROR::INVALID_TAG_NM:Record 1, Read name HWI-D00328:58:H7EAEADXX:2:1108:10580:81442, N…