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insaflu

INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

interartic

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

lineages

Resources for calling and describing the circulating lineages of SARS-CoV-2

llama

Local Lineage and Monophyly Assessment

long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline

longread_tutorials

Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data

measles

Nextstrain build for measles virus

measles_primers

Measles primer for full genome sequencing

medaka

Sequence correction provided by ONT Research

micall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

microgmt

Mutation tracker for microbial genomes

mikeroyal-bioinformatics-guide

mira

modkit

A bioinformatics tool for working with modified bases

mviest

membrane vesicle impact estimation

mytax

mytax is a tool for building custom taxonomies, useful for nucleotide sequence classification

nano-q

Python script for conservatively cleaning ONT reads from bam files and estimate variant frequencies.

nanomerge

Pipeline utility to perform merge of barcoded nanopore runs

nanomonsv

SV detection tool for nanopore sequence reads

nanopolish

Signal-level algorithms for MinION data

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

ncov-clades-schema

Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain

ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

nextclade

Viral genome alignment, clade assignment, mutation calling, and quality checks

ngspeciesid

Reference-free clustering and consensus forming of long-read amplicon sequencing

novel-sars-cov-2-p1-lineage-in-brazil

pango-designation

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