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Scripts to wrap Terra API calls for programmatic workflow execution, workspace management, and data export to other platforms. Part of the workflow is specific to my environment, but hopefully it a…

Python 4 Updated Jul 11, 2023

Build data reports in 100% Python (a fork of Datapane)

Python 42 1 Updated Jan 5, 2025
Python 1 1 Updated Dec 24, 2024

Simple test framework for Nextflow pipelines

Java 147 26 Updated Dec 28, 2024

The ARTIC field bioinformatics pipeline

Python 118 67 Updated Jan 7, 2025

Repository for suggesting new lineages that should be added to the current scheme

Jupyter Notebook 1,046 98 Updated Dec 21, 2024

a service to allow people to register primers to be monitored for intersecting variants and be notified if new variants arise

Ruby 3 3 Updated Nov 3, 2024
TypeScript 9 Updated Jan 7, 2025

Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification

Python 16 8 Updated Sep 27, 2023

Reorients assembled microbial sequences

Python 105 3 Updated Nov 22, 2024

a tool to filter sites in a FASTA-format whole-genome pseudo-alignment

Rust 40 1 Updated Nov 28, 2024

Predict MLST directly from uncorrected long reads

Python 26 6 Updated Mar 30, 2022

Follow up to Grace Blackwell's 661k dataset, for 2023

Python 86 5 Updated Dec 4, 2024

Bayesian inference of ancestral dates on bacterial phylogenetic trees

R 85 17 Updated Oct 16, 2024

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Python 126 33 Updated Oct 9, 2024

simple program to rotate a circular sequence to start at a given position or string

C 18 2 Updated Jul 9, 2023

Basic workflow for nanopore sequencing data

Nextflow 15 7 Updated Nov 7, 2024

resources for bioinformatics education

78 10 Updated Mar 15, 2024

Reads mapping against target sequences, checking mapping and consensus sequences production

C 8 6 Updated Dec 14, 2022

NCBI Pathogen Detection Portal toolkit

Perl 11 Updated Sep 6, 2023

A genome visualization python package for comparative genomics

Python 299 23 Updated Dec 22, 2024

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Python 252 38 Updated Jul 15, 2024

Ultra-deep search for novel viruses

Jupyter Notebook 263 34 Updated Mar 29, 2023
Nextflow 20 3 Updated Dec 12, 2024

Fast k-mer based tool for multi locus sequence typing (MLST)

Python 43 7 Updated Sep 3, 2020

Precise host read removal

Python 81 4 Updated Dec 20, 2024

Workflows and scripts for the assembly and analysis of SARS-CoV-2 whole genome tiled amplicon sequencing.

WDL 5 Updated Dec 20, 2024

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Dockerfile 197 126 Updated Jan 2, 2025

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

WDL 38 18 Updated Jan 6, 2025
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