frankambrosio3

Frank Ambrosio's starred repositories

Freyja-barcodes

Language:HTMLBSD-2-Clause200

verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Language:Python27400

datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Language:Jupyter NotebookNOASSERTION33500

sra-tools

SRA Tools

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mycosnp-nf

CDCgov/mycosnp-nf

Language:NextflowApache-2.03500

wf-ani

workflow for computing Average Nucleotide Identity (ANI) between FastA and GenBank files

Language:ShellApache-2.0300

Grandeur

UPHL's Reference Free Pipeline

Language:NextflowGPL-3.02300

long-read-pipelines

Long read production pipelines

Language:Jupyter NotebookBSD-3-Clause13000

Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Language:Python23100

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language:PythonBSD-3-Clause314300

pyMLST

whole genome MLST analysis

Language:PythonNOASSERTION3300

chewBBACA

BSR-Based Allele Calling Algorithm

Language:HTMLGPL-3.012900

tbdb

Standard database for the TBProfiler tool

Language:PythonLGPL-3.02800

awesome-README-templates

A collection of awesome readme templates to display on your github profile.

Language:JavaScriptMIT101200

awesome-github-profile-readme-templates

This repository contains best profile readme's for your reference.

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tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Language:PythonApache-2.02300

ngs-preprocess

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Language:NextflowGPL-3.03000

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?

CC0-1.09500

amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

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wf-assembly-snps

general workflow for genome assembly-based SNP phylogeny with optional recombination masking

Language:NextflowApache-2.0300

ecoli_serotyping

In silico prediction of E. coli serotype

Language:PythonApache-2.04600

nf-gpt

Experimental plugin to integrate GPT like prompt into Nextflow

Language:GroovyApache-2.01200

pipeline-resources

Bioinformatics Pipeline and Visualization resources

Apache-2.05200

GAS_identification

Language:WDLGPL-3.0600

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

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GAS_Scripts_Reference

Scripts and reference files to type Group A Streptococcus

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cgMLST-comparison

Language:Jupyter NotebookGPL-3.0300

performance_metrics

100

public_health_bacterial_genomics

Language:WDLAGPL-3.0100

rclone

"rsync for cloud storage" - Google Drive, S3, Dropbox, Backblaze B2, One Drive, Swift, Hubic, Wasabi, Google Cloud Storage, Azure Blob, Azure Files, Yandex Files

Language:GoMIT4548900