Artem Babaian
Artem Babaian
File format and software port compatibility matrix for bioSyntax. | | status | |---|:------------------| | X | Syntax Complete | | o | In Development | | - | Unavailable...
# Open TODO list A collection of tasks to improve bioSyntax. Feel free to tackle any of these if you'd like to pitch in. If there's no name/ID beside a...
Currently each instance is pulling an image from the `serratusbio` dockerhub repository. We can likely download this faster by pulling directly from ECR. This can be accomplished by: - [...
We need to migrate all the assembly and annotation data generated as part of Serratus to our data-lake in a structured way so as to allow for programmatic access. This...
[Explorer Link](https://serratus.io/explorer?run=SRR5121783#result) `Name: Pipistrellus bat coronavirus HKU5 isolate BY140535, complete genome` sequence identified from a Corn sequencing run [ SRR5121783](https://www.ncbi.nlm.nih.gov/sra/?term=SRR5121783). Run Info: `SRX2436954: High phosphate, lateral root, biol. Repl. 4`...
We are now generating novel CoV sequences that are of high quality (complete assembled genomes or near-complete genomes). High quality sequences like Frank (Fr4NK?) and Ginger need to be deposited...
When data is decompressed via `fastq-dump`, on `serratus-dl` a named pipe is created and the output fastq file is `split` into 1M reads per fastq-block. This is not written to...
There are edge-cases of instance errors in which say the `serratus-align` container is not doing any meaningful work (measured by CPU%) and the shut-down procedures fail to catch and gracefully...
Currently to get `serratus` up and running requires a few steps including building containers, uploading them, initializing AWS credentials and access keys, then submitting a job (sraRunInfo table) to the...
Heya, I'm leading up an analysis of RNA viruses across the Sequence Read Archive called [`Serratus`](https://www.nature.com/articles/s41586-021-04332-2). I've started going down the rabbit hole recently with creating a way of exploring...