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bacass

Simple bacterial assembly and annotation pipeline

civet

culebront_pipeline

A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.

degenprimergui

This is a graphical user interface for the DegenPrimer — multiplex PCR simulation with degenerate primers.

fieldbioinformatics

The ARTIC field bioinformatics pipeline

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..

long-read-assembler-comparison

Benchmarking of long-read assembly tools for bacterial whole genomes

longshot

diploid SNV caller for error-prone reads

lrbinner

LRBinner is a long-read binning tool that overcomes several limitations of our previous work MetaBCC-LR (ISMB 2020). The tool uses variational auto-encoders to bin error-prone long reads using coverage and composition.

masq

Multiplex Accurate Sensitive Quantitation (MASQ) analysis and primer design

miniforge

A conda-forge distribution.

monkeypox

Nextstrain build for mpox (monkeypox) virus

mpd-perl

Multiplex Primer Design

nanopanel2

Nanopanel2: a somatic variant caller for Nanopore panel sequencing data

nanortax

Real-time analysis pipeline for nanopore 16S rRNA data

oligomm-report

onepomodoro

OnePomodoro is just a simple podomoro technique app. Include some simple Pomodoro timers.

openprimer

An R Package for Multiplex PCR Primer Design and Analysis

optmage

Scripts for designing oligos and primers for MAGE (Multiplex Automated Genome Engineering)

p3wrapr

A python wrapper for primer3 - including primer checking and tagging

pcr_primers

primer design using primer3

plex_stats

Calculate primer stats for multiplex PCR primers.

pomoxis

Analysis components from Oxford Nanopore Research

porechop

adapter trimmer for Oxford Nanopore reads

poretools

a toolkit for working with Oxford nanopore data

primalscheme

A tool for designing multiplex PCR primers for generating tiling amplicons.

primer-algorithm

A primer design algorithm for Multiplex Polymerase Chain Reaction (PCR).

primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).

primer3-py

Simple oligo analysis and primer design