farhadm1990

nextflow

A DSL for data-driven computational pipelines

DAS_Tool

DAS Tool

biolecter.xt

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

htslib

C library for high-throughput sequencing data formats

panaroo

An updated pipeline for pangenome investigation

ggCaller

Bifrost graph gene caller.

snp-sites

Finds SNP sites from a multi-FASTA alignment file

pggb-paper

The PanGenome Graph Builder

circlator

A tool to circularize genome assemblies

pipeline-transcriptome-de

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

Roary

Rapid large-scale prokaryote pan genome analysis

pytmler

A python package to create tidy html-based reports

NanoOK

Analysis tool for Nanopore sequencing data

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

DnaFeaturesViewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

wf-bacterial-genomes

Small variant calling for haploid samples

Porechop

adapter trimmer for Oxford Nanopore reads

PyPore

A python tool box for fast and accurate quality control, conversion and alignment of nanopore sequencing data

pomoxis

Analysis components from Oxford Nanopore Research

pangenome

Renders a collection of sequences into a pangenome graph.

Assembly-Dereplicator

A tool for removing redundant genomes from a set of assemblies

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

ggcoverage

Visualize and annotate genomic coverage with ggplot2

readytowear

Ready-made Taxonomic Weights Repository