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pangolearn

Store of the trained model for pangolin to access.

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

phylo-io

Phylo.IO JS tree viewer

pimgavir

PIpeline for MetaGenomic Analysis of Viral reads from 2nd generation sequencer

porechop

adapter trimmer for Oxford Nanopore reads

porecov

SARS-CoV-2 workflow for nanopore sequence data

primalscheme

a tool for designing primer panels for multiplex PCR.

primer-schemes

Primer schemes for real-time genome epidemiology

public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

pyro-cov

Pyro models of SARS-CoV-2 variants

rima_pipeline

rnaseqworkflow

Roddy RNA-seq Workflow Plugin

sanbomics_scripts

scripts and notebooks from sanbomics

sars-cov-2

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures

sars-cov-2-africa-dashboard

sars-cov-2-contextual-data-specification

Collection template and associated materials for SARS-CoV-2 metadata

sars-cov-2-france

Epidémiologie Moléculaire du SARS-CoV-2 en France

sars-cov-2_gtg

Genomic Tech's COVID sequencing

sars-cov-2_sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

sars-cov-2_variant-reports

Informal summaries of notable SARS-CoV-2 lineages

sars-cov-3

SARs-CoV-2 Primer schemes

sarscov2recombinants

Scan SARS-SoV-2 sequences for potential recombinants

seqtk

Toolkit for processing sequences in FASTA/Q formats

sequana

Sequana: a set of Snakemake NGS pipelines

shanti

Shallow Nanopore Sequencing for Transcriptomics

simpitb

A pipeline for the analysis of whole genome sequences belonging to Mycobacterium tuberculosis complex

snipit

snipit: summarise snps relative to your reference sequence

spades

SPAdes Genome Assembler

sunbeam

A robust, extensible metagenomics pipeline

surpi

SURPI