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medaka

Sequence correction provided by ONT Research

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

metagenomics_workflows

Workflows for metagenomic sequence data processing and analysis.

mi_libro

mi_presentacion

bookdown edmo & xaringan

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

minion_qc

Quality control for MinION sequencing data

mirkwood

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

multi-metagenome

Scripts and tutorials on how to assemble individual microbial genomes from metagenomes

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

mummer

Mummer alignment tool

nanopolish

Signal-level algorithms for MinION data

nextdenovo

Fast and accurate de novo assembler for long reads

ninja-ops

Ninja Is Not Just Another OTU Picking Solution

ont_fast5_api

Oxford Nanopore Technologies fast5 API software

paletteer

🎨🎨🎨 Collection of most color palettes in a single R package

pantools

PanTools

patchwork

The Composer of ggplots

pgap

NCBI Prokaryotic Genome Annotation Pipeline

pilon

Pilon is an automated genome assembly improvement and variant detection tool

pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

pkgmetagenomica

What the Package Does (One Line, Title Case)

plotsr

Tool to plot synteny and structural rearrangements between genomes

porechop

adapter trimmer for Oxford Nanopore reads

prodigal

Prodigal Gene Prediction Software

progressivecactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules