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guppy_on_slurm

Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler

h-popg

H-PoP and H-PoPG: Heuristic Partitioning Algorithms for Single Individual Haplotyping of Polyploids

hardware_introduction

What scienfitic programmers must know about CPUs and RAM to write fast code.

haybaler

Haybaler: Collate/integrate reporting CSV or bam.txt files from the Wochenende pipeline https://github.com/MHH-RCUG/Wochenende

heatmaps

Heatmap script for Wochenende output files

home

DMR Identification Tool

hpc-intro

Intro to HPC lesson materials

java-genomics-toolkit

Collection of scripts for working with Wiggle files and analyzing sequencing data

jbrowse

A modern genome browser built with JavaScript and HTML5.

jbrowse-components

Monorepo with JBrowse 2 web, JBrowse 2 desktop, and more.

jbrowse2_utils

Bash scripts for writing assemblies and tracks to JBrowse2 https://jbrowse.org/jb2/

liftoff

An accurate GFF3/GTF lift over pipeline

mashtree

:deciduous_tree: Create a tree using Mash distances

masterblaster

A SLURM tool for performing parallel BLAST searches

megalodon

metarupore

scripts to get reference.fasta and target list for metagenomic adaptive nanopore sequencing of complicated environmental microbiome

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

modbam2bed

nanopolish

Signal-level algorithms for MinION data

nextflow

A DSL for data-driven computational pipelines

nf-blast

Work in progress - nextflow blast.

nf-co.re

Files for the main nf-core website >>>

nf-testdata

Test datasets for nextflow pipelines.

nf_wochenende

A nextflow version of the Wochenende reference metagenome binning and visualization pipeline

pantools

PanTools v0.1

prowlertrimmer

Trimming tool for Oxford Nanopore sequence data

raspir

Raspir, the rare species identifier

ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs

rs_demultiplex

Simple demultiplexing of FASTQ, one oligo (barcode) at a time