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Hi, I'm trying to do a n ANI Matrix usign this command line. but i have some problems.
I used this command line https://github.com/asadprodhan/Average-Nucleotide-Identity-ANI-analysis.git and I fol…
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Hi, thanks for developing this tool
I run the script of vcf2phylip.py successfully but found the output seems to be the amino acid sequences. My code and the screenshort of my output file are as fo…
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**Description**
**Sub-lineage of:** JN.1.4
**Earliest sequence:** 2024-9-20, Hong Kong, EPI_ISL_19464534
**Most recent sequence:** 2024-10-10, Hong Kong, EPI_ISL_19498393
**Continents circulatin…
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The new version of CUDASW 4.0 claims to support only protein chains.
What needs to be done to be able to search in the nucleotide database?
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I noticed we are missing some CCHF sequences , e.g. https://www.ncbi.nlm.nih.gov/nuccore/OQ633003.1. From the ingest logs after alignment we drop from 4760 segment sequences on NCBI virus (https://www…
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### TLDR
I accidentally misconfigured the ingest due to inconsistent casing of config values and it took way to long to find out what's wrong.
### What happened
I was setting up a Loculus ins…
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Hi everyone,
I want to create a database with all sequences of mithocondria from insects, like this:
```
haystac database \
--mode build --mtDNA \
--query '("Insecta"[Organism] AND …
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Hi David,
Thank you for your previous reply. I would really appreciate your help if you could clarify my following doubts:
1. Can orthofinder produce single copy orthologue file using the nucleotide…
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Hi there - I am using the very new version of the crabs package and have successfully gotten it running, have downloaded the NCBI taxonomy, and have downloaded sequences from BOLD. Now I am trying to …
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Currently seqkit seq filters by quality based on an average quality score. However, other tools such as FASTX's fastq_quality_filter, allow the user to select how many nucleotides (as a percentage) he…