USDA-VS

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13 repositories

Flumina
Public
A pipeline for the analysis of Illumina sequence data from Influenza viruses
R
•
GNU General Public License v3.0
•2•1•0•0•Updated Mar 5, 2026Mar 5, 2026
GenoFLU
Public
Influenza data pipeline to automate genotyping assignment
Python
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GNU General Public License v3.0
•10•40•2•0•Updated Mar 4, 2026Mar 4, 2026
vSNP3
Public
vSNP -- validate SNPs
bam-files snps pipeline
bam-files snps pipeline genomics phylogenetics influenza wgs high-throughput-sequencing bwa-mem tuberculosis
Python
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GNU General Public License v3.0
•2•12•8•0•Updated Feb 27, 2026Feb 27, 2026
vsnp3_test_dataset
Public
Dataset for testing vSNP version 3 installation
1•0•0•0•Updated Feb 9, 2026Feb 9, 2026
nvsl_bioinformatic_training
Public
The NVSL Bioinformatics Workshop will feature training on command-line bioinformatic tools, processes, and resources routinely used at NVSL for diagnostic testi…
HTML
•1•1•0•0•Updated Oct 15, 2024Oct 15, 2024
vSNP
Public
vSNP -- validate SNPs
bam-files snps pipeline
bam-files snps pipeline genomics vcf phylogenetics snp wgs high-throughput-sequencing high
Python
•
GNU General Public License v3.0
•12•22•4•0•Updated Sep 19, 2024Sep 19, 2024
NAHLN_AMR
Public
Python
•2•4•0•0•Updated Sep 7, 2022Sep 7, 2022
vSNP_reference_options
Public
vSNP supporting files
GNU General Public License v3.0
•2•0•0•0•Updated Sep 21, 2021Sep 21, 2021
minimum_fastqs
Public
testing files: smallest file size and still complete through vSNP_step1.py
1•0•0•0•Updated Jan 7, 2020Jan 7, 2020
vSNP_archive
Public
Archived versions of vSNP
Python
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Apache License 2.0
•1•0•0•0•Updated Jan 7, 2020Jan 7, 2020
vcf_test_files
Public
A small set of VCFs with expected output tables for script testing
1•0•0•0•Updated Jan 28, 2019Jan 28, 2019
fastq_data_set-brucella
Public
Brucella FASTQ test files
1•0•0•0•Updated Sep 17, 2018Sep 17, 2018
fastq_data_set-tb_complex
Public
1•0•0•0•Updated May 31, 2017May 31, 2017