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mosaik

reference-guided aligner for next-generation sequencing technologies

mummer

Mummer alignment tool

nanolyse

Remove lambda phage reads from a fastq file

nasopharyngeal-virome

nextflu

Real-time tracking of influenza evolution

nextstrain_base

pipeline components for realtime virus analysis

northernbug.github.io

The NorthernBUG Website

nucamino

A nucleotide to amino acid alignment program optimized for virus gene sequences.

oci-cli

Command Line Interface for Oracle Cloud Infrastructure

ohsnap

paml

This is code for running Orthofinder -> PAML

phylovega

Interactive tree visualizations in Python (powered by Vega).

pipeline-resources

Bioinformatics Pipeline and Visualization resources

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

primaschema

Generate primer scheme bundles from a YAML and BED file

primer-schemes

primer-schemes-pvh

Primer schemes for real-time genome epidemiology

ptrhash

PTRHash minimal perfect hash function, based of PTHash

pubtree

A hierarchical search tool for the Medline database

pyaranet4

A cross-platform Python interface for the Aranet4 CO₂ meter

pymummer

Python3 module for running MUMmer and reading the output

python-kmer-graph-generator

Annotated source of a kmer graph generator in Python

read-it-and-keep

Read contamination removal

runlistcompare

Python 3 port of runListCompare

sars-cov-2

SARs-CoV-2 Primer schemes

sars-cov-2-contextual-data-specification

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

sars2-seq-eval

Evaluation of SARS-CoV-2 sequencing protocols

seqanaltools

Command-line tools for analysing and manipulating sequence data, written for my own needs.

seqsum

Robust individual and aggregate checksums for nucleotide sequences