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I'd like to validate the utility of vg in the alignment of ancient DNA. The shortest path to this would be through simulation of aDNA-like reads. We already have the capacity to take recalibrated BAMs…
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I just saw the preprint and KAGE looks like a promising alternative to GATK.
Would it be possible to use KAGE to genotype ancient DNA samples? The golden standard at the moment seems to be pileupC…
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## Test cases
Linting
```bash
$ linkml lint ancient.yml
/home/james/git/mixs-minas/extension-ancient/src/mixs/schema/ancient.yml
warning Enum 'DamageTreatmentEnum' does not have recommend…
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#### Is your feature request related to a problem? Please specify.
Ancient DNA fragments are frequently shorter than the read length. For paired end reads, this results in R1 and R2 that overlap. O…
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Dear Erik,
Thanks for writing this tool!
I have a quick question regarding the use of this tool for ancient DNA data. Some of my work is on degraded DNA, which is typically log-normally distribu…
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### Description of feature
Due to the high fragmentation of ancient DNA data, there is not much gain in using long-read DNA sequencing methods for assembling ancient DNA samples. However, many ancien…
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We have already used metaGEM to assemble MAGs from ancient samples, e.g. [see zenodo repo](https://zenodo.org/record/7414438#.Y7l_CoLP3wc) & [github issue](https://github.com/kosticlab/ancient-microbi…
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## Context:
In ancient DNA studies, a popular field is to recover ancient pathogen genomes (e.g. [Yersinia pestis](http://dx.doi.org/10.1016/j.cub.2017.10.025)), i.e. the genomes of dead organisms …
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**New term details**
```
Term name - Conditions of Sample Storage
Structured comment name - storage_conditions
Definition - General conditions in which the sample was stored in long-term collect…
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**New term details**
For us to assess a new term request we require the following details:
```
Term name - Library reamplification polymerase
Structured comment name - lib_reamp_polymerase
Defini…